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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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