[gmx-users] Strange pullx coordinates (PMF calculations)

CROUZY Serge 119222 serge.crouzy at cea.fr
Wed Oct 31 16:43:23 CET 2018

Dear gromacs users

I've been running gromacs for several years, and enjoyed it..
I've been running PMF calculations for protein DNA interactions without problems until recently:
Now I'm puzzled with the X coordinates being written in the pullx files (and thus taken as reaction coordinate values in the PMF). This is my problem

I run two simulations 1)  protein A moving away from DNA                      DNA---A->  along x
                                       2) same protein A moving away from DNA in the presence of protein B:  B-DNA---A -> along x
In 2) A and B interact slightly and I expect to see a slight difference in the profiles for pulling A away
In both simulations I'm pulling on center of mass of A away from center of mass of DNA (force along X only)

My problem is that the x pulling coordinates in simulation 2) (in the pullx files) are around 9 A larger than in simulation 1). Consequence: the profiles are shifted along x by around 9 A. This is not logical to me since my reaction coordinate is distance between com of A and com of DNA which should be the same !!
It's as if the size of the simulation box (around 10 A larger in 2) to accommodate B ) mattered .. ?!  (I'm running PME with PBC in water...)

I hope this is clear enough and somebody can tell me what's happening ?!

Thanks a lot for your valuable answers


Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble  UMR  CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110
Tel (33) 438782963
Fax (33) 438785487

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