Visualizing your system would probably help here -- do you see air pockets?
Maybe if you increase the solvent buffer you'll start with a more favorable
density. You may just have to run for longer in order to equilibrate the
density. Does it look like the density has equilibrated?
Good luck!
Jason
On Mon, Aug 2, 2010 at 8:19 AM, Shubhra Gupta <shubhg.iiar.res.in> wrote:
> Dear Jason:
>
> I have solvated the disaccharide molecule using three point water model.
> Because the
> molecule is so small I used only buffer size of 7. That is why I am getting
> density of
> 0.6g/cm3. But in order to run NVT and NPT I need to increase density of the
> system to 1g/cm3.
> Using below given parameters I am able to increase density from 0.6 to 0.8
> in 5ps but not to 1.0
> Therefore what parameters should I add or reduced to get 1g/cm3 density in
> 5ps?
>
> &cntrl
> imin = 0, irest = 0, ntx = 1,
> ntt = 3, gamma_ln = 3.0,
> temp0 = 0.0,
> ntb = 2,
> ntp = 1,
> ntc = 2, ntf = 2,
> ntr = 0,
> taup = 0.7,
> dt = 0.001, nstlim = 5000,
> ntpr = 200, ntwr = 500, ntwx = 500
> &end
>
> Thanking you
>
> Shubhra
>
>
> On Mon, Aug 2, 2010 at 4:17 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > Where's the question? In any case, 0.6 seems a very very low density.
> Was
> > your system set up correctly? It sounds like you don't have nearly
> enough
> > waters for your box size. 5ps is probably not enough to increase your
> > density so dramatically.
> >
> > Good luck!
> > Jason
> >
> >
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 02 2010 - 06:00:24 PDT
