[gmx-users] Distance Restraints on Protein - possible at all?

NG HUI WEN HuiWen.Ng at nottingham.edu.my
Thu Feb 23 04:17:04 CET 2012

Dear Mark,

Thanks for contributing your ideas and suggestions, really appreciate it.

The reason I am playing with distance restraints on my protein is because I am interested to see the effects of equilibrating a protein in membrane using the two different restraint methods i.e. distance vs. position.

Yes, without distance restraint (i.e. removing disre = simple in the mdp) will allow the simulation to run to completion very smoothly.

I will give Berendsen pressure coupling a shot and see how it goes. However, prior to applying distance restraint on my protein, I have ran 5ns of position restraint simulation (with P-R coupling) and there weren't any complaints/problems.

Many thanks again for your help.


From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
Sent: Thursday, February 23, 2012 9:48 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Distance Restraints on Protein - possible at all?

On 22/02/2012 11:17 AM, NG HUI WEN wrote:

Sent: Sunday, February 19, 2012 1:19 PM
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: Distance Restraints on Protein - possible at all?

Dear gmxusers,

I have been trying to apply distance restraints on my protein but have been unsuccessful thus far.

For what purpose?

I have consulted the user forum previously and with some much-appreciated help I have managed to get my simulation (with distance restraints applied) to run. However, the joy did not last long as the simulation crashed very quickly (after ~40-50ps).

Do they run with no restraints?

P-R P-coupling is known to be unsuitable for equilibration (see manual), so that might be a factor here.

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