[gmx-users] Equilibration

‪farial tavakoli‬ ‪ farial.tavakoli at ymail.com
Thu Jul 13 17:21:49 CEST 2017

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
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?
Thanks in advanceFarial

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