Hi all,
> Dear Acoot
>
> this is a question for gromacs, NOT amber...
I agree, but will try to answer nevertheless:
>> rcoulomb = 1.0 ; Short-range electrostatic cut-off
>> rvdw = 1.0 ; Short-range Van der Waals cut-off
>> rcoulomb = 1.4 ; Short-range electrostatic cut-off
>> rvdw = 1.4 ; Short-range Van der Waals cut-off
>> The difference is the cut-off. One is 1.4,the other is 1.0. Can anyone
>> explain their difference on the influence of the MD result?
This cutoffs are not sharp cutoffs, but the distance at which your direct
space interaction transitions into the reciprocal part of PME or the
isotropic long range vdW correction. Ideally, changing the value would
make no difference for your simulation. However, since the long range
parts of the interactions are more approximate than the short range direct
space terms, making the cutoff too small introduces potential function
inaccuracies. Making it very large means a lot of pair-pair interaction
need to be computed, making your simulation slow and pushing your minimum
system box size.
In my experience, 8-10 Angstrom are reasonably conservative values for
this parameter (but note that Gromacs uses Nanometer here). I am not sure
that anyone would argue that using 14 Angstrom offers any real benefit for
an explicit solvent simulation. This is experience from using Amber, but
the same *should* hold true for Gromacs (but Adrian is right, the Gromacs
list may tell you more here)
>> Suppose I use AMBER 99SB force field, will you lease tell me how can
>> decide the value of the above cut-offs?
This is not really a force field related question. But you could check the
cutoff used to parameterize the force field and use that one. In practice
it should not make such a big difference.
If you are still unsure, why not run both and compare the results?
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Apr 10 2012 - 07:30:04 PDT
