Minor fixes of typos.

diff --git a/src/kernel/md.c b/src/kernel/md.c
index 8f6a0931d32bc61b919fe22f1e03d361e58d8ceb..c20d31f2e623d320383804071927961a3ee46d5a 100644 (file)
--- a/src/kernel/md.c
+++ b/src/kernel/md.c
@@ -435,7 +435,7 @@ static void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr,
     if (bTemp) 
     {
         /* Sum the kinetic energies of the groups & calc temp */
-        /* compute full step kinetic energies if vv, or if vv2 and we are computing the pressure with IR_NPT_TROTTER */
+        /* compute full step kinetic energies if vv, or if vv-avek and we are computing the pressure with IR_NPT_TROTTER */
         /* three maincase:  VV with AveVel (md-vv), vv with AveEkin (md-vv-avek), leap with AveEkin (md).  
            Leap with AveVel is also an option for the future but not supported now.  
            bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy. 
@@ -1055,7 +1055,7 @@ double do_md(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
     }
 
     /* md-vv uses averaged full step velocities for T-control 
-       md-vv2 uses averaged half step velocities for T-control (but full step ekin for P control)
+       md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
        md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
     bVV = EI_VV(ir->eI);
     if (bVV) /* to store the initial velocities while computing virial */

diff --git a/src/kernel/mdrun.c b/src/kernel/mdrun.c
index 679d4442b4b0090cb2b290767efb6e6dffd9e0d1..fa72979e8d0217696d01156eeff62066faf3ec8b 100644 (file)
--- a/src/kernel/mdrun.c
+++ b/src/kernel/mdrun.c
@@ -98,9 +98,9 @@ int main(int argc,char *argv[])
        "can be as high as 20 times, but in most other setups involving cutoffs and PME the",
        "acceleration is usually only 4~6 times relative to a 3GHz CPU.[PAR]",
        "Supported features:[PAR]",
-       " * Integrators: md, md-vv, md-vv2, sd and bd.\n",
+       " * Integrators: md/md-vv/md-vv-avek, sd/sd1 and bd.\n",
        " * Long-range interactions (option coulombtype): Reaction-Field, Ewald, PME.\n",
-       " * Temperature control: Supported only with the sd, bd, md-vv and md-vv2 integrators.\n",
+       " * Temperature control: Supported only with the md/md-vv/md-vv-avek, sd/sd1 and bd integrators.\n",
        " * Pressure control: Not supported.\n",
        " * Implicit solvent: Supported.\n",
        "A detailed description can be found on the website:\n",

diff --git a/src/kernel/openmm_wrapper.cpp b/src/kernel/openmm_wrapper.cpp
index 7dac71da09863b13bb1ea41e14fd89a7f521677b..8e8c3412def8072b96a585cb7f51d3fda7b505c8 100644 (file)
--- a/src/kernel/openmm_wrapper.cpp
+++ b/src/kernel/openmm_wrapper.cpp
@@ -334,7 +334,7 @@ void checkGmxOptions(t_inputrec *ir, gmx_localtop_t *top)
          (ir->eI !=  eiBD) 
        )
     {
-        gmx_fatal(FARGS, "OpenMM supports only the following integrators: md-vv/md-vvak, sd/sd1, and bd.\n");
+        gmx_fatal(FARGS, "OpenMM supports only the following integrators: md/md-vv/md-vv-avek, sd/sd1, and bd.\n");
     }
 
     /* Electroctstics */
@@ -353,7 +353,7 @@ void checkGmxOptions(t_inputrec *ir, gmx_localtop_t *top)
          (ir->eI !=  eiSD1)  && 
          (ir->eI !=  eiSD2)  && 
          (ir->eI !=  eiBD) ) 
-        gmx_warning("OpenMM supports only Andersen thermostat with the md-vv/md-vvak integrators.\n");
+        gmx_warning("OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.\n");
 
     if (ir->opts.ngtc > 1)
         gmx_fatal(FARGS,"OpenMM does not support multiple temperature coupling groups.\n");
@@ -727,7 +727,7 @@ void* openmm_init(FILE *fplog, const char *platformOptStr,
         static_cast<LangevinIntegrator*>(integ)->setRandomNumberSeed(ir->ld_seed); /* TODO test this */
     }
     else {
-        gmx_fatal(FARGS, "OpenMM supports only the following integrators: md-vv/md-vvak, sd/sd1, and bd.\n");
+        gmx_fatal(FARGS, "OpenMM supports only the following integrators: md/md-vv/md-vv-avek, sd/sd1, and bd.\n");
     }
 
     integ->setConstraintTolerance(ir->shake_tol);