[gmx-users] How to run NPT (anisotropic simulatio) for urea-water system with variable axis only in z direction

Sivashangari Gnanasambandam g0501135 at nus.edu.sg
Tue Jan 16 06:52:14 CET 2007


I am trying to study the dissolution of urea in water. After adding the
water molecule using genbox, I did the energy minimization by applying
pbc. Then I run the equilibration for 300ps using NPT anisotropic
pressure coulpling and variable axis only in the z direction. The
reference pressure is 1 bar. After the run, the cystal structure is
deformed (which should n't be).

The mdlog file shows the avg pressure in the range of 2-4e+2 bar.

I have attached my parameter file , please help me to find the solution
for my problem.

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Tuesday, January 16, 2007 1:41 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] infinitive force acting on atom during

Sivashangari Gnanasambandam wrote:
> Dear all,
> I run the NPT (anisotropic) for the urea-water system. After the md 
> run the pressure is not closer to 1 bar but in terms of 100. Suggest 
> me the corrections in my parameter file.

When you post to this list, please use a Subject for your email that is
relevant - please do not just reply to the last email you received and
change the topic. That way you stand a chance of someone who knows about
your problem reading it. This isn't a helpdesk and we aren't obliged to
help you, so you stand the best chance of being helped if you make life
simple for us.

Further, you'll need to provide a lot more information about what you're
trying to do in order for us to suggest where you might be wrong, in the
same way that ringing up a car mechanic and saying "my 1996 Toyota Camry
doesn't work" doesn't get you very far....

For a start, how did you equilibrate this system? How long did you then
run it for? Over how long did you collect your statistics for
calculating this pressure?

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