[gmx-users] Degrees of freedom for each atom ?

[Justin Lemkul]

On 4/15/14, 9:18 AM, diptipotdar wrote:
> Hi ,
> Is there any option in GROMACS to calculate degrees of freedom for each atom
> ?
> I am using constraints (LINCS-all bonds) in my MD simulation for ligands and
> water(SHAKE).
> I can see the total degrees of freedom from .log file. .But I am supposed to
> calculate the temperature of each atom in a group by using equipartition
> theorem by using velocities and masses.
> Is there any such option which will help me to calculate individual
> temperatures or degrees of freedom for each atom in my system ?
> My system contains metal cluster with ligands and water( as a solvent).The
> metal cluster is heated by thermostat and I am looking at heat transfer from
> metal cluster.
>

Use g_traj and correct for the constraints with a simple scaling factor:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2003-March/004870.html

-Justin

-- 
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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 601
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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