[gmx-users] Issues using tabulated potentials for coarse-grained simulation
tamisra1985 at gmail.com
Wed Jul 29 09:28:40 CEST 2015
Many thanks Brian !
On Tue, Jul 28, 2015 at 12:50 AM, Brian Yoo <Brian.S.Yoo.12 at nd.edu> wrote:
> Hi Tamrisa,
> 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
> > model
> > 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
> > without using separate temperature couplings for group molecules?
> > Thanks
> > Tamisra
> > --
> > --
> > Tamisra Pal
> > Post Doctoral Research Fellow
> > Technische Universität Darmstadt
> > Institut für Festkörperphysik
> > Hochschulstraße 6
> > 64289 Darmstadt , Germany
> > --
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