Dear Dr. Case
I am using a pre equilibrated DMPC bilayer from Dr. Phil Biggin's group in
Oxford.
Since I am removing a lot of lipids after inserting my protein, so I guess
you are right, I might have to equilibrate it more to adhere to lipid
parameters.
I haven't tried but will not try the image command in ptraj, thanks for that
suggestion, I had it in mind but it got slipped.
My pressure-time graph for 100 ps of NPT showed majority of the pressures in
-ve values ranging from 0 to -250 or so and very few values in +ve.
As you mentioned 100ps is a very small simulation for such a huge system
(with 62,000 atoms). So, I guess I have to equilibrate the system more, may
be on an order of few more hundreds of picoseconds before which the pressure
can be seen to be stabalized around 1 atm.
I do want to make sure, however, the following two points: >>>>>>>>>>>>
1. Since I am simulating a membrane protein, and my BOX is RECTILINEAR (as
mentioned in OUT file), I considered using ntp = 2 which is anisotropic
pressure scaling (Amber 8 manual says that this option can be used for
membrane proteins)? I want to confirm if it makes sense or shall I use ntp =
1?
2. In addition, I used taup = 2.0. In the mannual it says that deafult value
is 1.0 but higher values might be necessary if trajectories are
unstable. What should be the reasonable value of this parameter to be used
in membrane protein simulation?
Thanks a lot for your suggestions.
Best Regards
Akshay
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
David A. Case
Sent: Wednesday, February 14, 2007 5:05 PM
To: amber.scripps.edu
Subject: Re: AMBER: Membrane Simulation: NPT Issues
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
...good luck...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
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 | http://www.scripps.edu/case
==================================================================
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Received on Sun Feb 18 2007 - 06:07:20 PST
