[gmx-users] problem

Justin Lemkul jalemkul at vt.edu
Sun May 6 15:38:05 CEST 2018

On 5/6/18 9:31 AM, Alex wrote:
> Hi
> On Sat, May 5, 2018 at 1:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>> Hi,
>> I don't know of any forcefield that uses such nonbonded cutoffs, but that
>> should probably not of itself lead to instability. It will just be harder
>> to convince your reviewers that your simulation models reality.
> I do not understand what you mean, you mean the 1.3 nm for the rcoulomb and
> rvdw is not a good choice?

What prompted you to choose that value? Cutoffs are part of the force 
field; if you set values that are not in accordance with the force 
field's underlying parametrization convention, you can invalidate the 
physical model. rcoulomb is somewhat flexible when using PME, but in 
general, use what is prescribed unless you have demonstrated that 
whatever you're doing is superior.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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