Shyno Mathew wrote:
Hello Prof. David,
thanks for your reply.
I will try using isotropic pressure scaling. But still I am not clear
why the simulations ran fine with first .mdp file. As mentioned in the
previous email only few parameters were different in my .mdp file
compared to my advisor's.
I am just copying those parameters again:
Parameters that are different in my advisor's file:
DispCorr = Ener
tau_t = 0.20
compressibility = 5e-6 5e-6 5e-6 0 0 0
gen_vel = yes
gen_temp = 1
gen_seed = 473529
can including dispersion corrections for pressure induce such a huge change?
By changing several variables at once, it becomes hard (read: almost impossible)
to say what caused it. By also not generating velocities (assuming this is step
1 in equilibration), you can induce instability.
The real lesson is you shouldn't make haphazard changes or take anything for
granted as far as settings that "should work." Spending a few hours reading the
literature will save you weeks of troubleshooting an elusive problem.
-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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