[gmx-users] Equilibration

farial tavakoli farial.tavakoli at ymail.com
Fri Jul 14 13:17:06 CEST 2017

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }    Hi justin
 Thank you for replyActually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial in gromacs. And did all the steps and issued all commands that said in this tuturial . I also generated my ligand topology by PRODRG and edited the charges and charge groups . To edit atome charge, according to aminoacids.rtp file, i considered what my atomes are bonded to , in order to best give their charge. Then , regarding to the article : Practical considerations for building GROMOS-compatible small-molecule topologiesEditted the charge groups , but i think , maybe i was wrong in specifying charg groups. In addition, i noticed that there was a wrong bond in the gromacs topology ang gromacs cordinate files, so i corrected them but i dont know if i did right?  These are all that i did. I dont know more about generating ligand topology but informatin that said in this tuturial. If you let me, send my ligand topology file to you? 
With best regardsFarial

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On Friday, July 14, 2017, 2:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

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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