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. Cheers, Huiwen From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@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: From: NG HUI WEN Sent: Sunday, February 19, 2012 1:19 PM To: gmx-users@gromacs.org<mailto:gmx-users@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. Mark << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
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