[gmx-users] some question about REMD

Justin Lemkul jalemkul at vt.edu
Wed Oct 17 19:38:04 CEST 2012

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).


> 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


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