[gmx-users] comm-grps problem gromacs 4.0.4
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 29 13:40:10 CEST 2010
Oliver Grant wrote:
> Hi there,
> I'm running a 200ns simulation with a small trisaccharide in water. The
> trisacc drifts around the box. I've tried using comm-grps = System and
> comm-grps = <blank> and comm-grps = carb and what is below.
Why wouldn't your trisaccharide diffuse around? The only appropriate way to
treat your system is "comm-grps = System." Re-setting COM motion for different
components (in a normal aqueous system) is incorrect. Membranes are a different
story, but that's not important here.
> carb is the name I use in my top file and index file. For the index I
> specify the groups in make_ndx and then text edit the index file and
> change the name to carb. I've run this simulation on a different carb
> before but with integrator set to md and it worked fine.
What do you mean "worked fine"? Your sugar didn't diffuse around? I don't see
anything "wrong" with the behavior you've described yet.
> Tcoupl = berendsen
This parameter is ignored when using the sd integrator, just FYI.
> ; Groups to couple separately
> tc-grps = carb SOL Na
You should not couple ions separately from solvent:
> ; Time constant (ps) and reference temperature (K)
> tau_t = 0.1 0.1 0.1
When using sd, a small tau_t may lead to overdamping of the dynamics. I don't
know specifically what implication this might have on your results, but there
are a number of threads in the list archive that might give you some
information. I think the general suggestion is to use tau_t >= 1.0 with sd.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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