rajat desikan wrote:
Justin,I have a question. If we download files from Peter Tieleman's
website, all you get are .gro files, and no cpt files. Then what should
one do? Continue using the velocities in the .gro file?
Run a new equilibration. IIRC, those structures are the product of very short
(2 ns or so) simulations produced many years ago. More equilibration is
expected for more modern simulations.
-Justin
On Fri, Apr 13, 2012 at 5:28 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
James Starlight wrote:
Dear Gromacs Users!
I want to perform simulation of the pure bilayer surrounded by
water. I'm using already pre-equilibrated bilayers as the
initial structure. During conversion pdb-> gro -> pdb the
velocities from initial equilibration runs of the structure were
lost. Should I start generating
Relying on a .gro file to maintain velocities is a bad idea. The
values contained therein lack sufficient precision to be reliable.
You should be using .cpt files to continue runs to preserve the
previous ensemble, thus making the choice of coordinate file format
irrelevant.
this velocities in my production run ( gen_Vel= yes) or i must
do equilibration instead first to generate velocities? Finally
what length
A production run should not start with newly generated velocities.
Doing so destroys the initial equilibration, and if you haven't
taken care to preserve that anyway, you should probably just start
over and make proper use of .cpt files.
should this equilibration be to provide reasonable velocities
for futrher MD run if I would avoild long equilibration period
because of suitability of my initial model?
There is no universal answer to this question. It depends on your
criteria for convergence and contents of the system, among other
considerations.
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
========================================
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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