E. Nihal Korkmaz wrote:
Dear all,
This may sound stupid, but just to make sure that I am right track about
implicit solvent simulations, the set up involves
pdb2gmx
editconf
grompp
I mean, we still need to define the box dimensions by editconf and apply
periodicity, right?
Not usually. Proper settings usually include "pbc = no" and long cutoffs. This
has been discussed at length in the list archive.
Besides, what type of ensemble would be a good choice (NPT, NVT, etc)?
Typically NVT. There is nothing compressible for NPT to act upon - you have,
e.g., a protein in an imaginary bath of solvent. If you apply NPT conditions,
the box will just collapse in on itself.
-Justin
Best,
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644
Email: kork...@wisc.edu <mailto:kork...@wisc.edu>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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