[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

[Chitrita Dutta Roy]

Thanks a lot to both of you.

Chitrita.

On Wed, Mar 11, 2009 at 2:09 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Chitrita Dutta Roy wrote:
>
>> Hi Tsjerk,
>>
>> Did you mean to send you the md.mdp file that I used to run grompp for md
>> simulation? I am using Gromacs 4.0.2 versision. I am not very clear about
>> the parameters used in mdp files. So I am sending the mdp file here.
>>
>>
> Some consultation with the manual will provide you with the information to
> learn about these parameters.  They should not be set blindly!
>
> > cpp                   =  /usr/bin/cpp
>
> This is an example of one of the obsolete parameters no longer used in
> Gromacs 4.0.x, hence grompp told you it would be ignored.
>
>  Tcoupl                =  V-rescale
>> tau_t                 =  0.1    0.1
>> tc_grps               =  Protein    SOL
>> ref_t                 =  300        300
>>
>
> Here is the problem, as grompp pointed out to you.  You are controlling the
> temperature of both the Protein and solvent water (SOL).  But your system
> contains NA+, doesn't it?  So it is not part of any temperature coupling
> group.  Try "Protein Non-Protein" for simple aqueous systems with ions.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> 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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