Kishore wrote:
Dear All,
I am running MD simulations of an Alcohol Dehydrogenase ( a tetramer)
with the bound NADPH in explicit solvent. I am employing GROMOS96 43a1
force field for the simulations. I need a clarification on the CUT-OFFs
applicable for this force field. I have seen many people using *rvdw =
1.4* and* rcoulomb = 1.0 ( short range vander-waals and elctrostatics
cut-offs) *in all the .mdp files. In the tutorial I am following (Justin
Lemkul's - protein ligand complex)) he used *rvdw = 1.0* and *rcoulomb =
1.0* in case of energy minimisation and* rvdw = 1.4* and *rcoulomb =
0.9* in case of NVT/NPT equilibration and production MD run. So, someone
please clarify me what the widely accepted values for these two would
be. If at all I should use* rvdw = 1.4*, then should -d flag in editconf
The latter. EM is relatively insensitive to the cutoffs in my experience, so
1.0 is fine there. For the real MD, use the proper settings given in the
production MD .mdp file.
be atleast 1.4 or can it be less than that in the case of PBC conditions
enabled.
You simply have to ensure that your system's components never "see" one another.
In principle, you'd be safe setting -d 1.4 and have a maximum of 2.8 nm
between periodic images. That can result in a lot of wasted time doing
calculations on distant water molecules when the box size gets extremely large.
If the box size/shape will not change much (as is the case for most
well-equilibrated protein/water systems), you can get away with a shorter value
of -d, maybe 1.0 or so. Don't set it as low as 0.7 (such that the periodic
distance is exactly 1.4 nm, equal to the cutoff), because then any small
fluctuation can cause you problems.
-Justin
--
KRISHNA KISHORE@IIT-MADRAS
--
========================================
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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