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

Justin Lemkul jalemkul at vt.edu
Wed Oct 31 16:48:49 CET 2018

On 10/31/18 11:43 AM, CROUZY Serge 119222 wrote:
> 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...)

Yes, that makes sense. The first column(s) in pullx.xvg are whatever 
(x,y,z) components of the group0 COM. If your box is larger, then 
naturally the position is different. What should not be different is the 
relative DNA-A distance, which is the actual reaction coordinate. 
Absolute coordinates of any one species don't really matter.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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