alexanderwien2k at gmail.com
Sun May 6 15:48:14 CEST 2018
On Sun, May 6, 2018 at 9:37 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 5/6/18 9:31 AM, Alex wrote:
>> On Sat, May 5, 2018 at 1:14 PM, Mark Abraham <mark.j.abraham at gmail.com>
>>> 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
>> 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.
I see, I always imagined the higher the cut-off value the better, and did
not pay attention that it need also to fit with the used FF. Here I am
using the gromos54a7 FF. I am going to reduce it to around 0.9. Although I
do not think it can help with the LINC warning and crashing. So, do you
know what else might cause the problem here in spite of several round of
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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