Mark Abraham wrote:
On 11/02/2011 9:14 PM, Sanjay Kumar Upadhyay wrote:
Sorry, in previous mail i did not write md protocol in details what i
followed for simulation. after energy minimization steps i did PR for 200
ps and then run the production MD. Even i did vacuum energy minimization
before adding solvent for all systems. I used steep followed by cg for
prot-solvent energy minimization which reached up to minimum applied
force
100 KJ/mol/nm.
Your results suggest you did not equilibrate well enough. See the link I
gave last time.
Either that, or incorrect ligand parameters or .mdp settings are being applied,
breaking the force field model and causing the crash. Without seeing the .mdp
and relevant topology(ies), it's impossible to say.
-Justin
--
========================================
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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