[gmx-users] temperatures of residues

[Ali Mohyeddin]

Dear Justin,

Thanks for your reply.
Would you please help me how I can correct my calculated temperature for
constraints I used? In my mdp file I used lincs constraint for all bonds in
NVE ensemble. I used GROMOS forcefield to simulate Lysozyme protein.

Bests,
Mohyeddin

On Sat, Jan 16, 2016 at 4:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/15/16 11:28 PM, Ali Mohyeddin wrote:
>
>> Dear all,
>>
>> I am going to calculate the temperature distribution inside a protein
>> (temperatures of residues). Is there any command in gromacs to do that?
>> Any
>> suggestion is appreciated.
>>
>>
> gmx traj can calculate it from a .trr in which you have saved velocities.
> You will need suitable index groups for the residues and you will need to
> correct the output for any constraints used.
>
> -Justin
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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