[gmx-users] Position Restraints MD

Justin Lemkul jalemkul at vt.edu
Mon Sep 30 14:13:12 CEST 2019

On 9/28/19 2:10 AM, ISHRAT JAHAN wrote:
> Thank you sir for the valuable suggestions. I have done distance restraints
> on metal and some atoms of amino acids residue as follows-
> first generated the distance restrained .itp file using the command
> gmx genrestr -f file.gro -n asp83_OD1_Zn.ndx -o distance_restrain.itp
> -disre_dist 0.221 -disre_frac 0.221 -disre_up2 0.221 -fc 1000 1000 1000
> where 0.221 is the bond length between the OD1 and Zn, and similarly
> generated itp files for other atoms also and then added thes files in the
> .top file by changing the residue no. accordingly.
> perform full md but after the simulation run when i calculated the pairwise
> distance between these atoms it shows large fluctuations nearly 0.4 nm.
> Please tell whether position restraints have been applied on required atom
> or not. If this is not the correct procedure kindly tell the correct
> procedure.

I don't think there's any real need to run genrestr; just create the 
topology directive yourself. You can't set every value to the same thing 
(0.221), though. Distance restraints are active over a range - see the 

If you need help troubleshooting, you will need to provide the actual 
[distance_restraints] contents.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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