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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Received on Mon Aug 02 2010 - 05:30:06 PDT
