[gmx-users] enegry minimisation

Justin A. Lemkul jalemkul at vt.edu
Wed May 19 13:47:40 CEST 2010

sonali dhindwal wrote:
> Hello All
> This question may sound trivial to many, but as i am new to this field, 
> please help.
> I want to ask a question regarding my previous query of distortion of 
> protein strucutre after molecular dynamcs simulation.

Can you provide a link to your previous post, for reference?

> I have noticed that after enegry minimisation using steepest decent 
> algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
> So is it necessary to do enegry minimisation step before MD, because 
> this is my modeled protein, and i have  already done energy minimisation 
> using different program and after that I have done refinement also.

Have you added solvent or anything else to the protein model?  If so, then the 
answer is yes.  Solvation with a regularly-ordered lattice of solvent molecules 
can (and often does) lead to bad clashes with your protein structure, thus 
necessitating further minimization.

There are plenty of reasons why a protein structure might be unstable, most of 
them related to .mdp file settings, but you haven't posted those so there's no 
way to know if you're doing things correctly.


> Thanks and regards
> ^
> --
> Sonali Dhindwal


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list