Re: AMBER: Membrane Simulation: NPT Issues

From: David A. Case <>
Date: Wed, 14 Feb 2007 15:04:47 -0800

On Mon, Feb 12, 2007, Akshay Patny wrote:

> I am doing a GPCR membrane simulation.

This is likely to be a quite difficult problem, and my guess is that not
many amberites have tried it. So you will probably have to experiment some.
Make sure that you can simulate the membrane by itself, for example. There
are some tricky points (as I read the literature) to get the area per head
group correct.

> After stepwise minimization of my system, I did a 20ps NVT simulation from
> 0-100 K followed by an NPT simulation of 100 ps from 100-300K.
> Everything looked okay until 20ps NVT simulation (to 100K). However, when I
> applied NPT conditions and raised temp to 300K, the inner/outer water layers
> got displaced.

What do you mean by "got displaced"? Are you seeing this visually? If so,
did you use the image command in ptraj to move everything back to the primary
unit cell?

> 2.C. NOTE: My pressure/time graph also suggests
> that during last 100 ps, pressure has not be stabalized around 1 atm.

What does the plot look like? Note that you should expect to see large
fluctuations in the instantaneous pressure.

Note also that you are describing very short simulations. I don't want to
encourage you to waste CPU time, but it could be that you just haven't
equilibrated things yet. Remember that the readers of this list know only
what you tell them....

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  skype:                 dacase
La Jolla CA 92037  USA            |
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Received on Sun Feb 18 2007 - 06:07:12 PST
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