udaya kiran wrote:
Dear GROMACS users,
I am working on a cyclic peptide dynamics in DMSO solvent box with
ffG53a6 force filed. As the results are not satisfactory, I have
carried out the MD by restraining couple of hydrogen bonds. However,
the results are same as unrestrained calculations when I used the "fac"
values of 1 or 2, which correspond to force constants of 1000 kJ/mol or
2000 kJ/mol.
There are a number of parameters that influence how well distance restraints
work outside of the force constant multiplier.
Could you please clarify me regarding the optimum and the highest value
that can be used for "fac", which is the multiplication factor for
disres_fc ( = 1000 kJ/mol).
I doubt anyone has determined an optimum, nor would it likely be broadly
applicable. Theoretically, there is no maximum value. You can make a restraint
as rigid or as flexible as you like. But as I said, there are a number of
settings that influence the potential energy curve used for distance restraints.
Could you also inform about the forcefield that best handles the DMSO
solvent box MD runs and also hydrogen bonds.
You're not likely to get anyone on this list to do your homework for you. Look
for literature precedent - similar solutes and solvents, successes and failures,
etc. The 53A6 parameters for DMSO are quite good, so the problem may be the
protein force field itself or any of the numerous .mdp settings that can be
improperly assigned.
-Justin
yours sincerely,
uday.
--
========================================
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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