[gmx-users] Re: Why potential energy not in negative value?

Justin Lemkul jalemkul at vt.edu
Fri Nov 2 11:32:26 CET 2012

On 11/1/12 8:25 PM, shika wrote:
> Hi Justin,
> Thanks for your explaination..First of all i got the HFIP topology from
> this site which prof Alan give it to me
> compbio.biosci.uq.edu.au/atb/download.py?molid=6187#files
> Due to before this when i create the structure by using packmol and run it
> using gromacs the forcefield that i used is gromos not recognize the F
> atom.Thats y i use prof alan suggestion..If i use the prodrg server its
> just the united atom and what i need is all atom.
> I already discuss with my senior she said that i need to increase the emtol
> and also the emsteep.From what i understand the lower emtol is the best for
> minimization part.I'm still cant minimize it with the value pe that i
> satisfied with..

Increasing emtol will result in an even less desirable outcome; it will stop 
energy minimization prematurely.  I also doubt that increasing emstep will help 
at all.

> So can i just proceed with the heating part and then try the equilibration
> or not?i wont gve the negative impact for my system right?

Hard to say.  I would try a very gentle NVT equilibration with a small time step 
to see if the system re-orients itself in a more favorable way.  Monitor the 
potential energy along the course of the simulation to see how it changes.



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


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