hello Justin:
thanks a lot for kind reply.
I've got another question: how to disable PBC? shall I simply delete
"pbc=xyz" from .mdp file? I found that sometimes if we delete some
parameters from .mdp, gromacs will use the default instead of disable it.
thank you very much
best
Albert
On 10/17/2012 07:38 PM, Justin Lemkul wrote:
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
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