[gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.
Chitrita Dutta Roy
chitrita.md at gmail.com
Tue Mar 10 21:48:48 CET 2009
Thanks a lot to both of you.
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 A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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