[gmx-users] Problem running equilibration step

[Priyanka Patel]

Hello Felipe,

Thanks for quick response,

I have change my nvt.mdp file according to your instruction, but still
getting the following error;

Fatal error:
Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values


Priyanka


On Thu, Jul 16, 2015 at 4:15 PM, Felipe Merino <
felipe.merino at mpi-dortmund.mpg.de> wrote:

> Hi,
>
> The error is rather clear. There are atoms that are not coupled to any
> thermostat. In principle, you can set tc-grps to System and only give one
> tau and reference temperature and it will work. If you need a more
> elaborated scheme, them you can supply group definitions (if not available
> but default) with an index file.
>
> Felipe
>
> On 16/07/15 12:37, Priyanka Patel wrote:
>
>> Dear all,
>>
>> I am doing simulation of DNA nano-structure using Gromacs (VERSION 4.6.5)
>> by applying CHARMM26 force field and TIP4P water model. The energy
>> minimization step is working fine but i am facing problem during
>> equilibration step due to wrong *nvt.mdp* file.
>>
>> Can you please guide me, which kind of parameter should be change in
>> *nvt.mdp* file for DNA nano-structure MD simulation. I am following Justin
>> A. Lemkul's tutorial (Lysozyme in water) using following link;
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
>>
>> I am getting error like this;
>>
>> Fatal error:
>>
>> 318 atoms are not part of any of the T-Coupling groups
>>
>> My command line is like this;
>>
>> *grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr *
>>
>> I am also attaching the modified nvt.mdp file according to DNA MD
>> simulation requirement for your reference.
>>
>> I am working under the government organization, National center for Cell
>> Science meant for non-profit research. I shall be highly obliged if you
>> could help me to solve this problem.
>>
>>
>>
>>
>>
> --
> Felipe Merino
> Max Planck Institute for Molecular Physiology
> Department of Structural Biochemistry
> Otto-Hahn-Str. 11
> 44227 Dortmund
> Phone: +49 231 133 2306
>
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-- 
Regards,
Priyanka Patel
Mo:+91-8805811500