[gmx-users] Regarding trjconv

Gregory Poon gpoon at gsu.edu
Thu Nov 17 17:00:38 CET 2016

On 11/17/2016 10:19 AM, Justin Lemkul wrote:
> 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

I have also noticed that if use a PBC-corrected .xtc file for hbond 
against solvent molecules, it will often generate an error or crash the 
tool, which does not occur without trjconv.


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