[gmx-users] some question about REMD

Albert mailmd2011 at gmail.com
Wed Oct 17 19:43:59 CEST 2012

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

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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