Re: [AMBER] Gradually Compress Volume to Increase Density

From: Shubhra Gupta <shubhg.iiar.res.in>
Date: Mon, 2 Aug 2010 17:19:34 +0500

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
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