[gmx-users] difference in rvdw , rlist parameters in em and nvt steps
sadr.mahboobe1989 at gmail.com
Thu Feb 11 11:28:26 CET 2016
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?
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On Feb 11, 2016 12:22 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
On Thu, Feb 11, 2016 at 9:46 AM Mahboobe Sadr <sadr.mahboobe1989 at gmail.com>
> 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.
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