Jarmila Husby wrote:
Dear all,
I am setting-up a simulation of a protein-DNA complex using amber force
field.
In the manual (v4.5.3) I have found the recommended cutoff distances for
electrostatics - coulombtype using PME (rcoulomb=rlist=rvdw = 0.9nm)
with Gromos ff. However, I am aware the cutoff values are specific for
different forcefield and also the simulated system.
Since I am using the amber ff with Gromacs, I wanted to ensure I set-up
the correct cutoffs to prevent any potential artifacts, so I have
searched the manual, gmx-users old posts (gromacs wiki links do not work
any more) and papers, and I found all sorts of distances for the
non-bonded interactions tratment with PME (ranging from 1.0 to 1.4 nm).
With respect to the amber ff, I found a value of 0.8nm cutoff for the
PME in the Amber manual.
Could you please advise me on what would be the reasonable cutoff values
to choose for the protein-DNA system, with the use of Gromacs 4.5.3 and
amber ff?
All your comments will be greatly appreciated.
You haven't searched in the most important location yet - the primary literature
for your chosen force field (and there are subtle differences among the
different Amber force fields). It is generally recommended to follow the
protocols used to derive the force field, in the absence of any subsequent
modifications that demonstrate better results.
-Justin
Thank you
Jarmila
Jarmila Husby, PhD Candidate
CRUK PPI Drug Discovery/ BMSG Group
Department of Pharm & Biol Chemistry
The School of Pharmacy, University of London
email: jarmila.hu...@live.pharmacy.ac.uk
tel: (44) 0207 753 5996
--
========================================
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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