[gmx-users] temperatures of residues

[Justin Lemkul]

On 1/18/16 12:01 AM, Ali Mohyeddin wrote:
> 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.
>

Google knows :)  See, e.g. 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-July/090607.html 
and subsequent posts in that thread for more details.

-Justin

> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================