[gmx-users] Energy Minimisation and Equilibration Problems

[Justin A. Lemkul]

Nancy wrote:
> Hello,
> 
> I am trying to run equilibration on my solvated ethylene glycol 
> (ethanediol) system.  I started with an ethanediol mol2 file from which 
> topolbuild generated various files.  I used editconf to enlarge to box 
> of the "ethanediol.gro" file:
> 
> $ editconf -f ethanediol.gro -o ethanediol_box.gro -box 5 5 5
> 
> and then I used genbox to solvate it:
> 
> $ genbox -cp ethanediol_box.gro -cs spc216.gro -shell 1 -o 
> ethanediol_solv.gro -p ethanediol.top
> 
> I ran energy minimisation on it:
> 
> $ grompp -f minim.mdp -c ethanediol_solv.gro -p ethanediol.top -o em.tpr
> 
> my minim.mdp file is:

<snip>

> and the energies converge (although I think that the values are still 
> too large for this system):
> 
> ==========================
> Steepest Descents converged to Fmax < 1000 in 12 steps
> Potential Energy  = -1.1206108e+04
> Maximum force     =  9.4016180e+02 on atom 31
> Norm of force     =  3.4989252e+02
> ==========================
> 

This all seems reasonable to me.

<snip>

> nsteps        = 5000   
> dt        = 0.0002
> 

As I said before, 1 ps is too short to be meaningful for just about every system.

> rvdw        = 1.3       

Also, if using Gromos96, this value of rvdw is not strictly correct for this 
force field.

> 
> the system "blows up".  Addtionally, the structure of the solute is 
> incorrect (all atoms are bonded to each other).

Are you still getting LINCS warnings?  If so, try "constraints = all-bonds" 
instead of "constraints = all-angles."  With respect to the "bonds" they are 
simply an artefact of whatever visualization software you are using.  Bonds are 
not formed and broken in classical MD.  Again I ask, when looking at the 
trajectory, are you compensating for periodic boundary conditions properly using 
trjconv?

-Justin

> 
> Please advise on how to minimise such a system further, and as to why 
> the equilibration is so unstable.
> 
> Thank you.
> 
> Nancy
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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