[gmx-users] Equilibration

Justin Lemkul jalemkul at vt.edu
Fri Jul 14 12:29:11 CEST 2017

On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:
> Hi Justin
> Thank you so much for your reply about minimize ligand in vacuoaccording to :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>   I minimized my protein and ligand alone to fix the problem (  LINCS warning, ( one or more water molecules can not to be settled . check for bad contacts or reduce time step))I checked my protein in desired solvent as i noticed in the previous mail, and it was stable. i minimized my ligand too in vacuo with the .mdp file which you advised me, it was minimized well and monitored by pymol, its configuration was ok.
> In addition, I reduced the time step from 0,002 to 0.001 , but got the same error in 2 steps.then, reduced the temperature to 100 k , but the same error displayed again.
> Actually, I cant understand some advices and causes in this site. like:
> I dont understand  some of causes and advices in this site, include:1) you are doing particle insertion in free energy calculations without using soft core2) your position restraints are to coordinates too different from those present in the system3) Make sure the forces don't get that large

None of those are relevant.

> How can i make sure the forces dont get that large? I dont know what these 3 causes are.
>   I have not recognized where the problem is and fixed it yet. It is wasting my time a lot. My protein and ligand were intact . so what is its problem?would you please help me? and introduce me an appropriate reference to be expert in GROMACS?

Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?



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


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