On 10/17/12 1:35 PM, Albert wrote:
thank you all the same. I saw many people use Amber for REMD and few people use
Gromacs for REMD and the parameters is not easy reachable. However, what I found
is that Amber use cutoff=999
I am just wondering, shall I also use such big value for the following?
rlist = 999; short-range neighborlist cutoff (in nm)
rcoulomb = 999 ; short-range electrostatic cutoff (in nm)
rvdw = 999 ; short-range van der Waals cutoff (in nm)
thank you very much
For a non-periodic box, setting all cutoffs equal to zero accomplishes the same.
Both approaches seek "infinite" cutoffs (i.e., all interactions are calculated).
-Justin
On 10/17/2012 06:18 PM, saber naderi wrote:
I am no expert in implicit solvent simulations but I think for these
simulations it is better to use stochastic dynamic integrators with no
pbc (instead of NVT) and infinite (or very large) cut-off distances because
there is no actual water molecule in your simulation box and [normally] you
do not have to worry about the boundary effects.
For finding appropriate parameters, you should have a look at the Gromacs
manual and read the literature but if you need a quick example see below
(please note that this is just an example).
Cheers,
Saber
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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