shahid nayeem wrote:
Hi Justin
Should I try to do position restraint at 500k and then full MD simulation.
Always equilibrate under the conditions you wish to use prior to collecting data
under those conditions.
As for whether or not your force field is even valid at such high temperature is
another question, but I know there is a substantial body of literature regarding
high-temperature MD, so you may want to do some reading to understand the pros
and cons of what you're trying to do.
-Justin
shahid
On 4/27/10, *Justin A. Lemkul* <[email protected]
<mailto:[email protected]>> wrote:
shahid nayeem wrote:
My peptide is 26 residue alpha helix obtained from crystal
structure .pdb file. I am posting energy minimization, position
restarint and full MD simulation .mdp file
<snip>
ref_t = 300 300
Here, you're equilibrating at 300 K...
<snip>
ref_t = 500 500
and here, you're running MD at 500 K, without any equilibration in
between. That could be a problem, but more likely, the high
temperature is simply causing the structure to break down. Short
helices are usually not stable in isolation, and heating them to
extreme conditions will probably accelerate this process. The
various results you're seeing with different helices may just
reflect that you haven't simulated long enough to see convergence in
the structural features, but from what you've described, I expect
what you're seeing is entirely normal, and almost predictable.
-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
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========================================
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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