[gmx-users] Regarding trjconv

[Justin Lemkul]

On 11/17/16 10:13 AM, Apramita Chand wrote:
> Dear All,
> Thanks for your explanation, Erik. I just want to know whether applying
> trjconv will affect my calculations of other values like radial
> distribution functions ,hydrogen bond properties.
> Before applying trjconv,my protein molecule appears to be shifted partly
> out of the box . Should I be applying trjconv in this situation before
> calculation of properties? Is it necessary at all?
>

Nearly all GROMACS tools handle PBC automatically.  Only position-dependent 
properties like RMSD, RMSF, covariance, etc. are impacted by not accounting for 
PBC.  Anything related to distances like RDF, H-bonds, etc. requires no 
correction, but even if you do use trjconv, the results should come out the same.

-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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