Hello,
I would try to extend ACF window (10, 50, 200ps) but not too much since you
might end with integrating noise which would lead to overestimation of
viscosity. For water, 4ps seems to be ok but your liquid might have longer
ACF tail so you are actually getting seriously underestimated viscosi
I am wondering what you mean by 'proper dynamics', Chris? And in
general, what's the advantage of using sd integrator over md
integrator together with Nose-Hoover thermostat.
Thanks,
km.
On Fri, Nov 23, 2012 at 5:43 PM, Christopher Neale
wrote:
> I use the SD integrator with tau_t = 1.0 ps for a
Justin, Thank you very much. I assume that pairs in pairtypes are used to
calculate 1-4 VdW interactions only and do not influence calculations of
short range VdW?
Regards,
km.
On Wed, Aug 29, 2012 at 6:10 PM, Justin Lemkul wrote:
>
>
> On 8/29/12 11:37 AM, Krzysztof Murzyn wrote
Hi,
I want to influence slightly the way VdW interactions are calculated by
providing customized values of sigma/epsilon in [ pairtypes ]. I employ
OPLS/AA. The section of my molecule definition looks like, say:
[ pairtypes ]
CT CT 1 0.33 0.2
When I run grompp I get the following error message:
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