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
--
========================================
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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