[gmx-users] comm-grps problem gromacs 4.0.4

[Justin A. Lemkul]

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.

<snip>

> 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:

http://www.gromacs.org/Documentation/Terminology/Thermostats

> ; 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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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