[gmx-users] comm-grps problem gromacs 4.0.4

[Oliver Grant]

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.

Oliver

On 29 April 2010 12:40, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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