[gmx-users] T-coupling groups
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 18 22:03:11 CET 2010
Zuzana Benkova wrote:
> Dear GROMACS users,
> I have checked the mails in archive which deal with the problem I am
> facing but did not find the answer what I do wrong.
> I want to compile a PEO chain centered in box of 2900 water molecules.
> In my md.mdp the relevant section is as follows
> Tcoupl = nose-hoover
> tc-grps = PEO SOL
> tau_t = 0.1 0.1
> ref_t = 50 50
> gen_vel = yes
> gen_temp = 50 50
> I have generated an index file where I have defined the PEO group. The [
> SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms.
> This matches with the gro file. I tried to prepare a tpr file using
You shouldn't have to do this. By default, each moleculetype is given its own
default index group:
> grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p
> topol.top -o PEO18_2900TIP3P_50K
> and got message
> Program grompp, VERSION 4.0.3
> Source code file: readir.c, line: 1050
> Fatal error:
> 16 atoms are not part of any of the T-Coupling groups
> I tried the compilations with 4.0.3 and 4.0.5 versions but the message
> was the same.
This is not a version-specific bug, so I'd imagine not. There's something in
your system that is not coupled. Perhaps you've done something wrong in setting
the index groups. Try without an index file (see above comment). If there's
something else in the system, it needs to be accounted for.
> I would be really thankful for an advice which can move me further.
> Thank you in advance.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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