[gmx-users] difference in rvdw , rlist parameters in em and nvt steps

M S sadr.mahboobe1989 at gmail.com
Thu Feb 11 11:50:51 CET 2016


Thanks for replying so fast.

Sent using Boxer

On Feb 11, 2016 2:05 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:

Hi,

That's up to the author of the tutorial. Smaller list sizes are faster to
run, and if the purpose of the EM is to ensure that equilibration succeeds,
then anything that works, works.

Mark

On Thu, Feb 11, 2016 at 11:28 AM M S <sadr.mahboobe1989 at gmail.com> wrote:

> I thought  the tutorial set the em parameters lower than nvt parameters
> based on a specific reason. So there is no specific reason in tutorial?
>
> Best regards
>
> Sent using Boxer
>
> On Feb 11, 2016 12:22 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> Hi,
>
> On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr <sadr.mahboobe1989 at gmail.com
> >
> wrote:
>
> > Dear all users,
> >
> > In mdp files in ligand tutorial,  rvdw,rlist.are equal to 1 in em step,.
> > And are equal to 1.4 in nvt,npt and production md
> >
> > When we can set different interaction parameters for different step?
> >
>
> You should choose such parameters based on those used for the
> parametrization of the force field, and/or subsequent reports of successful
> applications of them, particularly by the original authors.
>
> As you no doubt learned from the tutorial, EM is commonly used for relaxing
> inconsistencies in the starting geometry so that equilibration can proceed
> stably. Experience shows that short-range settings that are ultra faithful
> to the force field do not materially improve the success of equilibration -
> anything normally does the job fine.
>
> Mark
>
> Best regards
> > --
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