[gmx-users] Issues using tabulated potentials for coarse-grained simulation
Brian.S.Yoo.12 at nd.edu
Mon Jul 27 21:20:21 CEST 2015
Sorry for the slow response. Was a bit busy this weekend. I'm guessing you
are using Bhargava and Klein's model? I made a mistake in setting the
number of exclusions to 3 rather than 2 for their model. After I made that
change, things ended up working out. If you are using the SDK water model,
I should mention I also had some issues of the water freezing depending on
how I set my initial conditions. Annealing the system resolved that issue
(~400 K for a few ns).
Hope this helps!
On Saturday, July 25, 2015, Tamisra Pal <tamisra1985 at gmail.com> wrote:
> Hi Brian :
> I am also having a similar kind of issue in running a simulation of CG
> Ionic liquid molecules having tabulated 9-6 LJ potential . Surprisingly , I
> find that the density steadily increasing even after 30 ns , and the box
> length consequently decreasing . Though the temperature , pressure are OK .
> In my case I have used tc-grps = system .
> Can you tell me how to resolve this issue ? Are there any other techniques
> without using separate temperature couplings for group molecules?
> Tamisra Pal
> Post Doctoral Research Fellow
> Technische Universität Darmstadt
> Institut für Festkörperphysik
> Hochschulstraße 6
> 64289 Darmstadt , Germany
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