[gmx-users] Re: Why potential energy not in negative value?
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
> 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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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