[gmx-users] comm-grps problem gromacs 4.0.4

[Justin A. Lemkul]

Oliver Grant wrote:
> Thanks for the help,
> 
> With center of mass removal option I thought my sugar would stay in the 
> center of the box. It does in the first simulation I ran however what I 
> mean by diffuse is that it leaves the box on one side and enters from 
> the other. There is nothing physically wrong with this but I'd like the 
> center of mass removal to keep the sugar in the center.
> 

This is just a simple matter of periodic boundary conditions:

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

You can post-process the trajectory with, i.e. trjconv -center to keep the sugar 
in the center of the box, but this is really only useful for visualization purposes.

-Justin

> Oliver
> 
> On 29 April 2010 12:40, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================