Nicholas Breen. This fixes bug 435.
*/
extern bool zoom_3d(t_3dview *view,real fac);
-/* Zoom in or out with factor fac, returns TRUE when zoom succesful,
+/* Zoom in or out with factor fac, returns TRUE when zoom successful,
* FALSE otherwise.
*/
extern bool make_backup(const char * file);
extern FILE *ffopen(const char *file, const char *mode);
-/* Return a valid file pointer when succesfull, exits otherwise
+/* Return a valid file pointer when successful, exits otherwise
* If the file is in compressed format, open a pipe which uncompresses
* the file! Therefore, files must be closed with ffclose (see below)
*/
extern void init_multisystem(t_commrec *cr,int nsim,int nfile,
const t_filenm fnm[], bool bParFn);
-/* Splits the communication into nsim seperate simulations
+/* Splits the communication into nsim separate simulations
* and creates a communication structure between the master
* these simulations.
* If bParFn is set, the nodeid is appended to the tpx and each output file.
extern "C" {
#endif
-/* All functions return 1 if succesfull, 0 otherwise
+/* All functions return 1 if successful, 0 otherwise
* bOK tells if a frame is not corrupted
*/
# taken directly from ifp43a1.dat. For a description of what the numbers
# mean, see the GROMOS96 manual and the fie ifp43a1.dat
-# set the input seperator to #--- so we read one atom entry at a time
-# make sure the records are actually seperated by #---\n and not by say #--\n!!
-# don't put a seperator at the end of the file, only between records
+# set the input separator to #--- so we read one atom entry at a time
+# make sure the records are actually separated by #---\n and not by say #--\n!!
+# don't put a separator at the end of the file, only between records
$/= "#---\n";
# start arrays with 1 instead of 0
f.getRESname(f.all[resnum]) # residue name
f.getNATOM (f.all[resnum]) # number of atoms
- if f.nlin != 0: # 0 for a seperate molecule
+ if f.nlin != 0: # 0 for a separate molecule
f.getEXCLUS(f.all[resnum]) # number of exclusions
f.getATOM (f.all[resnum]) # atoms => f.atoms
in sequence are usually close in space too (e.g. a water molecule).
To this end, the <i>xdr</i> library is extended with a special routine
to write 3-D float coordinates. This routine was written by Frans van Hoesel
-as part of an Europort project, and can be obt
ianed through <a href="http://hpcv100.rc.rug.nl/xdrf.html">this link</a>.
+as part of an Europort project, and can be obt
ained through <a href="http://hpcv100.rc.rug.nl/xdrf.html">this link</a>.
<p>
All the data is stored using calls to <i>xdr</i> routines.
<h3>Using xtc in your "C" programs</h3>
To read and write these files the following "C" routines are available:
<pre>
-/* All functions return 1 if succesfull, 0 otherwise */
+/* All functions return 1 if successful, 0 otherwise */
extern int open_xtc(XDR *xd,char *filename,char *mode);
/* Open a file for xdr I/O */
if (debug) {
fprintf(debug,"searching residue: %4s atom: %4s\n",resnm,atomnm);
if (j == NOTFOUND)
- fprintf(debug," not succesful\n");
+ fprintf(debug," not successful\n");
else
fprintf(debug," match: %4s %4s\n",ap->resnm[j],ap->atomnm[j]);
}
return 0;
}
- /* next test isn't usefull in the case of C language
+ /* next test isn't useful in the case of C language
* but is used for the Fortran interface
* (C users are expected to pass the address of an already allocated
* XDR staructure)
static int xyz_first_x(FILE *status, const output_env_t oenv,
real *t, rvec **x, matrix box)
/* Reads status, mallocs x, and returns x and box
- * Returns natoms when succesful, FALSE otherwise
+ * Returns natoms when successful, FALSE otherwise
*/
{
int m;
fprintf(fp,"\\subsection{Simulation settings}\n");
fprintf(fp,"A total of %g ns were simulated with a time step of %g fs.\n",
ir->nsteps*ir->delta_t*0.001,1000*ir->delta_t);
- fprintf(fp,"Neighborsearching was performed every %d steps.\n",ir->nstlist);
+ fprintf(fp,"Neighbor searching was performed every %d steps.\n",ir->nstlist);
fprintf(fp,"The %s algorithm was used for electrostatic interactions.\n",
EELTYPE(ir->coulombtype));
fprintf(fp,"with a cut-off of %g nm.\n",ir->rcoulomb);
"radii) and atoms outside the box (these may occur often and are",
"no problem). If velocities are present, an estimated temperature",
"will be calculated from them.[PAR]",
- "If an index file is given it's contents will be sumamrized.[PAR]",
+ "If an index file, is given its contents will be summarized.[PAR]",
"If both a trajectory and a tpr file are given (with [TT]-s1[tt])",
"the program will check whether the bond lengths defined in the tpr",
"file are indeed correct in the trajectory. If not you may have",
"non-matching files due to e.g. deshuffling or due to problems with",
"virtual sites. With these flags, gmxcheck provides a quick check for such problems.[PAR]"
- "The program can compare run two input ([TT].tpr[tt], [TT].tpb[tt] or",
+ "The program can compare two run input ([TT].tpr[tt], [TT].tpb[tt] or",
"[TT].tpa[tt]) files",
"when both [TT]-s1[tt] and [TT]-s2[tt] are supplied.",
"Similarly a pair of trajectory files can be compared (using the [TT]-f2[tt]",
"For free energy simulations the A and B state topology from one",
"run input file can be compared with options [TT]-s1[tt] and [TT]-ab[tt].[PAR]",
"In case the [TT]-m[tt] flag is given a LaTeX file will be written",
- "consisting a rough outline for a methods section for a paper."
+ "consisting of a rough outline for a methods section for a paper."
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffOPTRD },
"with a disulfide brigde or intermolecular distance restraints.[PAR]",
"pdb2gmx will also check the occupancy field of the pdb file.",
- "If any of the occupanccies are not one, indicating that the atom is",
+ "If any of the occupancies are not one, indicating that the atom is",
"not resolved well in the structure, a warning message is issued.",
"When a pdb file does not originate from an X-Ray structure determination",
"all occupancy fields may be zero. Either way, it is up to the user",
write_sto_conf(ftp2fn(efSTO,NFILE,fnm),title,atoms,x,NULL,ePBC,box);
printf("\t\t--------- PLEASE NOTE ------------\n");
- printf("You have succesfully generated a topology from: %s.\n",
+ printf("You have successfully generated a topology from: %s.\n",
opt2fn("-f",NFILE,fnm));
if (watstr[0] != NULL) {
printf("The %s force field and the %s water model are used.\n",
}
if (nlines > 0)
sfree(lines);
- fprintf(stderr,"%d out of %d lines of %s converted succesfully\n",
+ fprintf(stderr,"%d out of %d lines of %s converted successfully\n",
n,nlines,sbfile);
*nspecbond = n;
else if (!b1 && b2)
fprintf(stdout,"\nEnd of file on %s but not on %s\n",fn1,fn2);
else if (!b1 && !b2)
- fprintf(stdout,"\nFiles read succesfully\n");
+ fprintf(stdout,"\nFiles read successfully\n");
else {
cmp_real(stdout,"t",-1,fr1->t,fr2->t,ftol,abstol);
cmp_int(stdout,"step",-1,fr1->step,fr2->step);
"tpbconv can edit run input files in four ways.[PAR]"
"[BB]1st.[bb] by modifying the number of steps in a run input file",
"with option [TT]-nsteps[tt] or option [TT]-runtime[tt].[PAR]",
- "[BB]2st.[bb] (OBSOLETE) by creating a run input file",
+ "[BB]2nd.[bb] (OBSOLETE) by creating a run input file",
"for a continuation run when your simulation has crashed due to e.g.",
"a full disk, or by making a continuation run input file.",
"This option is obsolete, since mdrun now writes and reads",
"When pressure and/or Nose-Hoover temperature coupling is used",
"an energy file can be supplied to get an exact continuation",
"of the original run.[PAR]",
- "[BB]3nd.[bb] by creating a tpx file for a subset of your original",
+ "[BB]3rd.[bb] by creating a tpx file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
"your tpx file, or when you want to make e.g. a pure Ca tpx file.",
"[BB]WARNING: this tpx file is not fully functional[bb].",
- "[BB]4rd.[bb] by setting the charges of a specified group",
+ "[BB]4th.[bb] by setting the charges of a specified group",
"to zero. This is useful when doing free energy estimates",
"using the LIE (Linear Interaction Energy) method."
};
for every atom we add all the contributions to this atom from all the different eigenvectors.
NOTE: one could add directly to the forcefield forces, would mean we wouldn't have to clear the
- field forces_cart prior the computation, but momentarily we want to compute the forces seperately
+ field forces_cart prior the computation, but momentarily we want to compute the forces separately
to have them accessible for diagnostics
*/
int j,eig;
case 3: xs[i]=C[s]*pM[s];xc[i]=oK[s]; xl[i]=pK[s];break;
}
}
- /*input order is different for test programm to match FFTW order
+ /*input order is different for test program to match FFTW order
(important for complex to real)*/
if (plan->flags&FFT5D_BACKWARD) {
rotate(xs);
typedef struct gmx_qhop_db_t *gmx_qhop_db;
-/* Return database if succesfull, or NULL on failure */
+/* Return database if successful, or NULL on failure */
extern gmx_qhop_db gmx_qhop_db_read(char *forcefield);
-/* Write the database to a filename. Return 1 on succes, or 0 for
+/* Write the database to a filename. Return 1 on success, or 0 for
failure */
extern int gmx_qhop_db_write(char *fn,gmx_qhop_db qdb);
/* Destroy the internal datastructures to free memory. Return 1 on
- succes, 0 for failure */
+ success, 0 for failure */
extern int gmx_qhop_db_done(gmx_qhop_db qdb);
/* Return the number of states in the database for a given residue
grid->dc_nalloc = 0;
if (debug)
- fprintf(debug,"Succesfully freed memory for grid pointers.");
+ fprintf(debug,"Successfully freed memory for grid pointers.");
}
int xyz2ci_(int nry,int nrz,int x,int y,int z)
/* Lennard-Jones coefficients */
snew(qm->c6,nr);
snew(qm->c12,nr);
- /* do we optimize the QM seperately using the algorithms of the QM program??
+ /* do we optimize the QM separately using the algorithms of the QM program??
*/
qm->bTS = ir->opts.bTS[grpnr];
qm->bOPT = ir->opts.bOPT[grpnr];
dump_nblist(debug,cr,fr,0);
if (bVerbose)
- fprintf(stderr,"Succesfully made neighbourlist\n");
+ fprintf(stderr,"Successfully made neighbourlist\n");
}
bool bXor(bool b1,bool b2)
{ "-beginfit", FALSE, etREAL, {&acf.tbeginfit},
"Time where to begin the exponential fit of the correlation function" },
{ "-endfit", FALSE, etREAL, {&acf.tendfit},
- "Time where to end the exponential fit of the correlation function, -1 is till the end" },
+ "Time where to end the exponential fit of the correlation function, -1 is until the end" },
};
#define NPA asize(acfpa)
t_pargs *ppa;
nparm = nfp_ffn[eFitFn];
if (debug) {
fprintf(debug,"There are %d points to fit %d vars!\n",ndata,nparm);
- fprintf(debug,"Fit to function %d from %g thru %g, dt=%g\n",
+ fprintf(debug,"Fit to function %d from %g through %g, dt=%g\n",
eFitFn,begintimefit,endtimefit,dt);
}
{
static const char *desc[] = {
"[TT]g_anaeig[tt] analyzes eigenvectors. The eigenvectors can be of a",
- "covariance matrix ([TT]g_covar[tt]) or of a Normal Modes anaysis",
+ "covariance matrix ([TT]g_covar[tt]) or of a Normal Modes analysis",
"([TT]g_nmeig[tt]).[PAR]",
"When a trajectory is projected on eigenvectors, all structures are",
"[TT]-first[tt] to [TT]-last[tt].",
"The projections of a trajectory on the eigenvectors of its",
"covariance matrix are called principal components (pc's).",
- "It is often useful to check the cosine content the pc's,",
+ "It is often useful to check the cosine content of the pc's,",
"since the pc's of random diffusion are cosines with the number",
"of periods equal to half the pc index.",
"The cosine content of the pc's can be calculated with the program",
"A line in the input file may start with a time",
"(see option [TT]-time[tt]) and any number of y values may follow.",
"Multiple sets can also be",
- "read when they are seperated by & (option [TT]-n[tt]),",
+ "read when they are separated by & (option [TT]-n[tt]),",
"in this case only one y value is read from each line.",
"All lines starting with # and @ are skipped.",
"All analyses can also be done for the derivative of a set",
"g_analyze always shows the average and standard deviation of each",
"set. For each set it also shows the relative deviation of the third",
- "and forth cumulant from those of a Gaussian distribution with the same",
+ "and fourth cumulant from those of a Gaussian distribution with the same",
"standard deviation.[PAR]",
"Option [TT]-ac[tt] produces the autocorrelation function(s).[PAR]",
{ "-e", FALSE, etREAL, {&te},
"Last time to read from set" },
{ "-n", FALSE, etINT, {&nsets_in},
- "Read # sets seperated by &" },
+ "Read # sets separated by &" },
{ "-d", FALSE, etBOOL, {&bDer},
"Use the derivative" },
{ "-dp", FALSE, etINT, {&d},
"It should be noted that the indexfile should contain",
"atom-triples for angles or atom-quadruplets for dihedrals.",
"If this is not the case, the program will crash.[PAR]",
- "With option [TT]-or[tt] a trajectory file is dumped containing cos and"
+ "With option [TT]-or[tt] a trajectory file is dumped containing cos and "
"sin of selected dihedral angles which subsequently can be used as",
"input for a PCA analysis using [TT]g_covar[tt]."
};
const char *desc[] = {
"g_bond makes a distribution of bond lengths. If all is well a",
"gaussian distribution should be made when using a harmonic potential.",
- "bonds are read from a single group in the index file in order i1-j1",
- "i2-j2 thru in-jn.[PAR]",
+ "Bonds are read from a single group in the index file in order i1-j1",
+ "i2-j2 through in-jn.[PAR]",
"[TT]-tol[tt] gives the half-width of the distribution as a fraction",
"of the bondlength ([TT]-blen[tt]). That means, for a bond of 0.2",
"a tol of 0.1 gives a distribution from 0.18 to 0.22.[PAR]",
"When the [TT]-mol[tt] option is given clusters will be made out of",
"molecules rather than atoms, which allows clustering of large molecules.",
"In this case an index file would still contain atom numbers",
- "or your calculcation will die with a SEGV.[PAR]",
+ "or your calculation will die with a SEGV.[PAR]",
"When velocities are present in your trajectory, the temperature of",
"the largest cluster will be printed in a separate xvg file assuming",
"that the particles are free to move. If you are using constraints,",
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of levels of grey in xpm output" },
{ "-ndf", FALSE, etINT, {&ndf},
- "Number of degrees of freedom of the entire system for temperature calculation. If not set the number of atoms times three is used." },
+ "Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used." },
{ "-rgblo", FALSE, etRVEC, {rlo},
"RGB values for the color of the lowest occupied cluster size" },
{ "-rgbhi", FALSE, etRVEC, {rhi},
else {
i0 = max(0,nbegin);
i1 = min(nx-1,nbegin+nsmooth);
- printf("Making smooth transition from %d thru %d\n",i0,i1);
+ printf("Making smooth transition from %d through %d\n",i0,i1);
for(i=0; (i<i0); i++)
combined[i]=y[i];
for(i=i0; (i<=i1); i++) {
"For an estimate of the error you can run g_statistics on the",
"ACF, and use the output thus generated for this program.",
"The functional forms of the available functions are:[PAR]",
- "One parmeter : y = Exp[-a1 x]",
- "Two parmeters : y = a2 Exp[-a1 x]",
- "Three parmeter: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x]",
- "Startvalues for the fit procedure can be given on the commandline.",
+ "One parameter : y = Exp[-a1 x],",
+ "Two parameters : y = a2 Exp[-a1 x],",
+ "Three parameters: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x].",
+ "Start values for the fit procedure can be given on the command line.",
"It is also possible to fix parameters at their start value, use -fix",
"with the number of the parameter you want to fix.",
"[PAR]",
"numerical derivative of the combination data/fit.",
"The second file contains the real and imaginary parts of the",
"frequency-dependent dielectric constant, the last gives a plot",
- "known as the Cole-Cole plot, in which the imaginary",
+ "known as the Cole-Cole plot, in which the imaginary",
"component is plotted as a function of the real component.",
"For a pure exponential relaxation (Debye relaxation) the latter",
- "plot should be one half of a circle"
+ "plot should be one half of a circle."
};
t_filenm fnm[] = {
{ efXVG, "-f", "dipcorr",ffREAD },
"option -corr is used. The output file name is given with the [TT]-c[tt]",
"option.",
"The correlation functions can be averaged over all molecules",
- "([TT]mol[tt]), plotted per molecule seperately ([TT]molsep[tt])",
+ "([TT]mol[tt]), plotted per molecule separately ([TT]molsep[tt])",
"or it can be computed over the total dipole moment of the simulation box",
"([TT]total[tt]).[PAR]",
"Option [TT]-g[tt] produces a plot of the distance dependent Kirkwood",
{ "-mumax", FALSE, etREAL, {&mu_max},
"max dipole in Debye (for histrogram)" },
{ "-epsilonRF",FALSE, etREAL, {&epsilonRF},
- "epsilon of the reaction field used during the simulation, needed for dieclectric constant calculation. WARNING: 0.0 means infinity (default)" },
+ "epsilon of the reaction field used during the simulation, needed for dielectric constant calculation. WARNING: 0.0 means infinity (default)" },
{ "-skip", FALSE, etINT, {&skip},
"Skip steps in the output (but not in the computations)" },
{ "-temp", FALSE, etREAL, {&temp},
const char *bugs[] =
{
"For complex molecules, the periodicity removal routine may break down, "
- "in that case you can use trjconv" };
+ "in that case you can use trjconv." };
static real dist = 0.0, rbox = 0.0, to_diam = 0.0;
static bool bNDEF = FALSE, bRMPBC = FALSE, bCenter = FALSE, bReadVDW =
FALSE, bCONECT = FALSE;
{ "-skip", FALSE, etINT, {&skip},
"Skip number of frames between data points" },
{ "-mean", FALSE, etBOOL, {&bMeanEmtx},
- "with -groups extracts matrix of mean energies in stead of "
+ "with -groups extracts matrix of mean energies instead of "
"matrix for each timestep" },
{ "-nlevels", FALSE, etINT, {&nlevels},"number of levels for matrix colors"},
{ "-max",FALSE, etREAL, {&cutmax},"max value for energies"},
/* Calculate the time difference */
delta_t = t - start_t;
- fprintf(stdout,"\nStatistics over %s steps [ %.4f thru %.4f ps ], %d data sets\n",
+ fprintf(stdout,"\nStatistics over %s steps [ %.4f through %.4f ps ], %d data sets\n",
gmx_step_str(nsteps,buf),start_t,t,nset);
calc_averages(nset,edat,nbmin,nbmax);
};
const char *bugs[] = {
- "The program should allow for random displacement off lattice points." };
+ "The program should allow for random displacement of lattice points." };
int vol;
t_atoms *atoms; /* list with all atoms */
for(i=0; (i<ddd->nhydro[id]); i++)
if (ddd->hydro[id][i] == ih) {
- printf("Hm. This isn't first time I find this donor (%d,%d)\n",
+ printf("Hm. This isn't the first time I found this donor (%d,%d)\n",
ddd->don[id],ih);
break;
}
"into hydrogen bonds. Ordering is identical to that in [TT]-hbn[tt]",
"index file.[BR]",
"[TT]-dan[tt]: write out the number of donors and acceptors analyzed for",
- "each timeframe. This is especially usefull when using [TT]-shell[tt].[BR]",
+ "each timeframe. This is especially useful when using [TT]-shell[tt].[BR]",
"[TT]-nhbdist[tt]: compute the number of HBonds per hydrogen in order to",
"compare results to Raman Spectroscopy.",
"[PAR]",
"Number of threads used for the parallel loop over autocorrelations. nThreads <= 0 means maximum number of threads. Requires linking with OpenMP. The number of threads is limited by the number of processors (before OpenMP v.3 ) or environment variable OMP_THREAD_LIMIT (OpenMP v.3)"},
#endif
{ "-NN", FALSE, etENUM, {NNtype},
- "HIDDENDo a full all vs all loop and estimsate the interaction energy instead of having a binary existence function for hydrogen bonds. NOT FULLY TESTED YET! DON'T USE IT!"},
+ "HIDDENDo a full all vs all loop and estimate the interaction energy instead of having a binary existence function for hydrogen bonds. NOT FULLY TESTED YET! DON'T USE IT!"},
{ "-gemfit", FALSE, etBOOL, {&bGemFit},
"With -gemainate != none: fit ka and kd to the ACF"},
/* { "-gemlogstart", FALSE, etREAL, {&logAfterTime}, */
int gmx_helixorient(int argc,char *argv[])
{
const char *desc[] = {
- "g_helixorient calculates coordinates and direction of the average",
+ "g_helixorient calculates the coordinates and direction of the average",
"axis inside an alpha helix, and the direction/vectors of both the",
"alpha carbon and (optionally) a sidechain atom relative to the axis.[PAR]",
"As input, you need to specify an index group with alpha carbon atoms",
"with multiple atoms in the first group is counted as one contact",
"instead of as multiple contacts.",
"With [TT]-or[tt], minimum distances to each residue in the first",
- "group are determined and plotted as a function of reisdue number.[PAR]",
+ "group are determined and plotted as a function of residue number.[PAR]",
"With option [TT]-pi[tt] the minimum distance of a group to its",
"periodic image is plotted. This is useful for checking if a protein",
"has seen its periodic image during a simulation. Only one shift in",
"generic trajectory. The number of intermediates can be controlled with",
"the -ninterm flag. The first and last flag correspond to the way of",
"interpolating: 0 corresponds to input structure 1 while",
- "1 corresponds to input strucutre 2.",
+ "1 corresponds to input structure 2.",
"If you specify first < 0 or last > 1 extrapolation will be",
"on the path from input structure x1 to x2. In general the coordinates",
"of the intermediate x(i) out of N total intermidates correspond to:[PAR]",
"gyration tensors are written.",
"With option [TT]-i[tt] the mean square internal distances are",
"written.[PAR]",
- "With option [TT]-p[tt] the presistence length is determined.",
+ "With option [TT]-p[tt] the persistence length is determined.",
"The chosen index group should consist of atoms that are",
"consecutively bonded in the polymer mainchains.",
- "The presistence length is then determined from the cosine of",
+ "The persistence length is then determined from the cosine of",
"the angles between bonds with an index difference that is even,",
"the odd pairs are not used, because straight polymer backbones",
"are usually all trans and therefore only every second bond aligns.",
"This will calculate the rotational correlation function using a first",
"order Legendre polynomial of the angle of a vector defined by the index",
"file. The correlation function will be fitted from 2.5 ps till 20.0 ps",
- "to a two parameter exponential",
+ "to a two parameter exponential.",
""
rm_pbc(&top.idef,ePBC,natoms,box,x,x);
- /* Dynamically build the ref tripels */
+ /* Dynamically build the ref triples */
if ( mode == 2 )
{
isize[NDX_REF1]=0;
/* Calculate the mean probability density */
- fprintf(stderr,"\nNumber of configuations used for SDF: %d\n",(int)normfac);
+ fprintf(stderr,"\nNumber of configurations used for SDF: %d\n",(int)normfac);
normfac = nbin[0]*nbin[1]*nbin[2] / normfac;
"file to work. ",
"You have to setup 4 groups in the index file before using g_sdf: [PAR]",
"The first three groups are used to define the SDF coordinate system.",
- "The programm will dynamically generate the atom tripels according to ",
+ "The program will dynamically generate the atom triples according to ",
"the selected -mode: ",
"In -mode 1 the triples will be just the 1st, 2nd, 3rd, ... atoms from ",
"groups 1, 2 and 3. Hence the nth entries in groups 1, 2 and 3 must be from the",
"Use -bin to set the binwidth for grid.[PAR]",
"The output will be a binary 3D-grid file (gom_plt.dat) in the .plt format that can be be",
"read directly by gOpenMol. ",
- "The option -r will generate a .gro file with the reference molecule(s) transfered to",
+ "The option -r will generate a .gro file with the reference molecule(s) transferred to",
"the SDF coordinate system. Load this file into gOpenMol and display the",
"SDF as a contour plot (see http://www.csc.fi/gopenmol/index.phtml for ",
"further documentation). [PAR]",
"Here is what some of the file options do:[BR]",
"-oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used.[BR]",
"-od: Distance between two groups. Distance is taken from the center of one group to the center of the other group.[BR]",
- "-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given seperately.[BR]",
+ "-od1: If one plane and one vector is given, the distances for each of the atoms from the center of the plane is given separately.[BR]",
"-od2: For two planes this option has no meaning."
};
"A line in the input file may start with a time",
"(see option [TT]-time[tt]) and any number of y values may follow.",
"Multiple sets can also be",
- "read when they are seperated by & (option [TT]-n[tt]),",
+ "read when they are separated by & (option [TT]-n[tt]),",
"in this case only one y value is read from each line.",
"All lines starting with # and @ are skipped.",
"[PAR]",
{ "-ttol", FALSE, etREAL, {&ttol},
"Tolerance on time in appropriate units (usually ps)" },
{ "-n", FALSE, etINT, {&nsets_in},
- "Read # sets seperated by &" },
+ "Read # sets separated by &" },
{ "-d", FALSE, etBOOL, {&bDer},
"Use the derivative" },
{ "-bw", FALSE, etREAL, {&binwidth},
"append output to an existing trajectory file.",
"No checks are performed to ensure integrity",
"of the resulting combined trajectory file.[PAR]",
- "Option [TT]-sep[tt] can be used to write every frame to a seperate",
+ "Option [TT]-sep[tt] can be used to write every frame to a separate",
".gro, .g96 or .pdb file, default all frames all written to one file.",
"[TT].pdb[tt] files with all frames concatenated can be viewed with",
"[TT]rasmol -nmrpdb[tt].[PAR]",
"* [TT]whole[tt] only makes broken molecules whole.[PAR]",
"Option [TT]-ur[tt] sets the unit cell representation for options",
"[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
- "All three options give different results for triclinc boxes and",
+ "All three options give different results for triclinic boxes and",
"identical results for rectangular boxes.",
"[TT]rect[tt] is the ordinary brick shape.",
"[TT]tric[tt] is the triclinic unit cell.",
"will be stored in the B-factor field in order to color with e.g. rasmol.",
"[PAR]",
"With option [TT]-nshell[tt] the number of molecules within a shell",
- "of radius [TT]-r[tt] around the refernce group are printed."
+ "of radius [TT]-r[tt] around the reference group are printed."
};
static int na=3,ref_a=1;
static real rcut=0;
/* Find start and end of longest helix fragment */
check_ahx(nres,bb,x,&hstart,&hend);
}
- fprintf(stderr,"helix from: %d thru %d\n",
+ fprintf(stderr,"helix from: %d through %d\n",
bb[hstart].resno,bb[hend].resno);
for(j=0,i=hstart; (i<=hend); i++) {
if (bHesse)
for (i=0; vecs[i]; i++) {
if (vecs[i]<7)
- gmx_fatal(FARGS,"ERROR: You have choosen one of the first 6 eigenvectors of the HESSE Matrix. That does not make sense, since they correspond to the 6 rotational and translational degrees of freedom.\n\n");
+ gmx_fatal(FARGS,"ERROR: You have chosen one of the first 6 eigenvectors of the HESSE Matrix. That does not make sense, since they correspond to the 6 rotational and translational degrees of freedom.\n\n");
values[i]=eigval[1][vecs[i]-1]/kT;
}
else
for (i=0; vecs[i]; i++) {
if (vecs[i]>(neig-6))
- gmx_fatal(FARGS,"ERROR: You have choosen one of the last 6 eigenvectors of the COVARIANCE Matrix. That does not make sense, since they correspond to the 6 rotational and translational degrees of freedom.\n\n");
+ gmx_fatal(FARGS,"ERROR: You have chosen one of the last 6 eigenvectors of the COVARIANCE Matrix. That does not make sense, since they correspond to the 6 rotational and translational degrees of freedom.\n\n");
values[i]=1/eigval[1][vecs[i]-1];
}
/* free memory */
snew(xav,natoms);
snew(vav,natoms);
read_conf(fngro,buf,&natoms,xav,vav,box);
- fprintf(stderr,"Succesfully read average positions (%s)\n",buf);
+ fprintf(stderr,"Successfully read average positions (%s)\n",buf);
EV=read_ev(fndat,natoms);
- fprintf(stderr,"Succesfully read eigenvectors\n");
+ fprintf(stderr,"Successfully read eigenvectors\n");
snew(index,nev);
for(i=0; (i<nev); i++)
}
ffclose(in);
}
- fprintf(stderr,"\rSuccesfully read eigenvector projections\n");
+ fprintf(stderr,"\rSuccessfully read eigenvector projections\n");
return evprj;
}
gf[i]=y;
}
ffclose(in);
- fprintf(stderr,"Succesfully read gamma\n");
+ fprintf(stderr,"Successfully read gamma\n");
return gf;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff