Essential dynamics: fixed restarts when ED group has > 1 molecule

[alexxy/gromacs.git] / src / tools / gmx_make_edi.c

diff --git a/src/tools/gmx_make_edi.c b/src/tools/gmx_make_edi.c
index 4da7814f2ad1b8d339b83405c8af048630987a5f..3ea5828637bba53be0229f0fc090c1975a0749fe 100644 (file)
--- a/src/tools/gmx_make_edi.c
+++ b/src/tools/gmx_make_edi.c
@@ -473,7 +473,7 @@ int gmx_make_edi(int argc,char *argv[])
   static const char *desc[] = {
       "[TT]make_edi[tt] generates an essential dynamics (ED) sampling input file to be used with [TT]mdrun[tt]",
       "based on eigenvectors of a covariance matrix ([TT]g_covar[tt]) or from a",
-      "normal modes anaysis ([TT]g_nmeig[tt]).",
+      "normal modes analysis ([TT]g_nmeig[tt]).",
       "ED sampling can be used to manipulate the position along collective coordinates",
       "(eigenvectors) of (biological) macromolecules during a simulation. Particularly,",
       "it may be used to enhance the sampling efficiency of MD simulations by stimulating",
@@ -518,10 +518,16 @@ int gmx_make_edi(int argc,char *argv[])
       "before a new cycle is started.[PAR]",
       "Note on the parallel implementation: since ED sampling is a 'global' thing",
       "(collective coordinates etc.), at least on the 'protein' side, ED sampling",
-      "is not very parallel-friendly from an implentation point of view. Because",
+      "is not very parallel-friendly from an implementation point of view. Because",
       "parallel ED requires some extra communication, expect the performance to be",
-      "lower as in a free MD simulation, especially on a large number of nodes. [PAR]",
-      "All output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a .edo file. In the output",
+      "lower as in a free MD simulation, especially on a large number of nodes and/or",
+      "when the ED group contains a lot of atoms. [PAR]",
+      "Please also note that if your ED group contains more than a single protein,",
+      "then the [TT].tpr[tt] file must contain the correct PBC representation of the ED group.",
+      "Take a look on the initial RMSD from the reference structure, which is printed",
+      "out at the start of the simulation; if this is much higher than expected, one",
+      "of the ED molecules might be shifted by a box vector. [PAR]",
+      "All output of [TT]mdrun[tt] (specify with [TT]-eo[tt]) is written to a [TT].edo[tt] file. In the output",
       "file, per OUTFRQ step the following information is present: [PAR]",
       "[TT]*[tt] the step number[BR]",
       "[TT]*[tt] the number of the ED dataset. ([BB]Note[bb] that you can impose multiple ED constraints in",
@@ -537,7 +543,7 @@ int gmx_make_edi(int argc,char *argv[])
       "is kept in that region.",
       "[PAR]",
       "The origin is normally the average structure stored in the [TT]eigvec.trr[tt] file.",
-      "It can be changed with [TT]-ori[tt] to an arbitrary position in configurational space.",
+      "It can be changed with [TT]-ori[tt] to an arbitrary position in configuration space.",
       "With [TT]-tau[tt], [TT]-deltaF0[tt], and [TT]-Eflnull[tt] you control the flooding behaviour.",
       "Efl is the flooding strength, it is updated according to the rule of adaptive flooding.",
       "Tau is the time constant of adaptive flooding, high [GRK]tau[grk] means slow adaption (i.e. growth). ",