bharat gupta wrote:
Hi
I did a simulation of 3 ns with OPLS AA 2001 Force Field for a protein
of 230 aa and also I carried out a simulation of 10ns for the same
protein but with different force field (Amber 2006) . I obtained the
rmsd of the trajectories of both simulation , which I found to be
different ?? i.e. 3ns rmsd from one simulation doesnot superimpose with
another (10ns) .. why there is such a difference ??
Different force fields can give different results, unfortunately. There are
several comparisons in the literature among common force fields. Understanding
inherent limitations and assumptions in each model is an important (read:
absolutely critical) part of designing a simulation.
Also realize that you're comparing an extremely short (3 ns) trajectory with a
moderately short (10 ns) one. In theory, exhaustive sampling (i.e. orders of
magnitude larger than what you've done) should converge over all simulations.
But due to the inherent differences in parameter sets, this is unlikely to be
the case. The fact that your simulations are so short probably magnifies this
effect.
-Justin
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
