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

[Mark Abraham]

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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