[gmx-users] error comm-grps=Protein SOL

M. Emal Alekozai memala at gmx.net
Thu Aug 7 22:48:59 CEST 2008

Dear All,

I have in a mdrun.mdp file following settings: 
   ; mode for center of mass motion removal =
    comm-mode                = Linear
   ; number of steps for center of mass motion removal =
   nstcomm                  = 1
   ; group(s) for center of mass motion removal =
   comm-grps                = Protein SOL

This causes following warning/ error in the log file:
   Large VCM(group SOL): -0.00020, 0.00161, 0.00109, T-cm: inf
   Large VCM(group rest): -0.00238, -0.01596, -0.10896, T-cm: inf
   Large VCM(group SOL): 0.00006, 0.00002, -0.00005, T-cm: inf
   Large VCM(group rest): -0.00009, 0.00483, 0.00106, T-cm: inf

For a small testrun on 8 CPU (xtc: 2MB, trr: 22MB) I get 8 logfiles which are due to this warnings 160 Mb each.
I looked the error Message up in the Gromacs mailinglist and found following question [2] but no solution :-( .
The Gromacs manual also didn't helped, there was only one line on page 137.

1: http://www.Gromacs.org/pipermail/gmx-users/2008-April/033316.html

If I use in the mdrun.mdp file one of the following options "comm-grps=Protein" or "comm-grps=SOL" or "comm-grps=SYSTEM" or ";comm-grps=" the warning does not appear in the log file.

I would like to know:

1. What does the option "comm-grps = Protein SOL" physical mean?
a) Does it mean:
The protein and solvent atoms may have a initial drift. Merge all PROTEIN and SOL atoms into a single group. Calculate the center of mass of this merged group and reset the center of mass motion of this merged group in every step?

b) Or does it mean:
For example because of initial setup "error" all the solvent atoms have a global drift in one direction and all the protein atoms have a drift in a other direction.
Calculate for both groups seperatly the center of mass and remove for each group the center of mass motion seperatly.

2. If the option "comm-grps = Protein SOL" physical means (1b) what do I have to change in my simulation setup to avoid the warnings/ error "T-cm: inf" in the log files?

3. Are the messages "... T-cm: inf" in the logfile a error or just a warning. Can I just ignore the messages or do I have to adjust my inputfile?

4. If I'm allowed to ignore the warning, how do I tell Gromacs not to write them in the log file. For a middle size simulation the logfile will use up my entire diskspace before the simulation has ended. 


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