[gmx-users] temperature of a single water molecule

[Justin Lemkul]

On 7/14/16 1:48 AM, Ali Mohyeddin wrote:
> Dear all,
>
> I am going to calculate the temperature of single water molecule around a
> protein by writing a simple script to calculate the temperature from
> what "trjconv"
> command prints out:
>
>   mass vx vy vz
> 2SOL OW 16 0.2789 -0.4959 0.8134
> 2SOL HW1 1 1.0917 1.3308 0.0835
> 2SOL HW2 1 0.1324 1.9991 -0.6413
>
>
>
>
>
>
> I set the "constraints = none" in mdp file. When I consider 9 DOF to
> calculate the temperature,  it is a different T than what "gmx energy"
> gives when I define a energy group for a single water molecule.
>
> Any response for the reason would be appreciated.
>

Setting "constraints = none" does not cause your water to become flexible.  In 
each water topology, the molecules are defined as rigid in #ifdef blocks that 
specify SETTLE to be used.  Unless you explicitly made the waters flexible with 
the right "define" keyword (which you shouldn't do during MD, because all the 
water models in GROMACS are intended to be rigid), then your waters are rigid. 
Hence the mismatch between the two results.

-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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