[gmx-users] Different results from identical tpr after MD

Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have

Re: [gmx-users] Different results from identical tpr after MD

bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further

Re: [gmx-users] Different results from identical tpr after MD

Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system

Re: [gmx-users] Different results from identical tpr after MD

Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories... On 2012-04-05 11:38:20PM +0530, bipin singh wrote: Thanks for the reply. * *I read the link. So, how

Re: [gmx-users] Different results from identical tpr after MD

That's an interesting philosophical question. In this case, you'll wind up with a 50 ns trajectory where each configuration is consistent with the thermodynamic ensemble you're approximating. That's as close a definition to realistic as I think is worth worrying about. You'd only need to worry

Re: [gmx-users] Different results from identical tpr after MD

...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 6 April 2012 4:20 AM Subject: Re: [gmx-users] Different results from identical tpr after MD Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples

Re: [gmx-users] Different results from identical tpr after MD

Sent: Friday, 6 April 2012 4:24 AM Subject: Re: [gmx-users] Different results from identical tpr after MD That's an interesting philosophical question. In this case, you'll wind up with a 50 ns trajectory where each configuration is consistent with the thermodynamic ensemble you're

Re: [gmx-users] Different results from identical tpr after MD

mesoscale approaches may perform better. -Justin Cheers, Acoot *From:* Matthew Zwier mczw...@gmail.com *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, 6 April 2012 4:24 AM *Subject:* Re: [gmx-users] Different results from identical tpr after MD That's

Re: [gmx-users] Different results from identical tpr after MD

bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather

Re: [gmx-users] Different results from identical tpr after MD

] Different results from identical tpr after MD bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines?  which depends more on the environment of the computer

Re: [gmx-users] Different results from identical tpr after MD

*Subject:* Re: [gmx-users] Different results from identical tpr after MD bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more

Re: [gmx-users] Different results from identical tpr after MD

energy change included. I am looking forward to getting more feedback on this topic. Acoot From: Peter C. Lai p...@uab.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 6 April 2012 4:20 AM Subject: Re: [gmx-users] Different results from identical tpr after

[gmx-users] Different results from identical tpr after MD

Dear Acoot: The idea of convergence is this: start a large number of simulations from different conformations, analyze some quantity over time in each simulation, and when the deviation of the average value of that quantity from each separate simulation is less than the time-variance

Re: [gmx-users] Different results from identical tpr after MD

Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such research article then please send me the

Re: [gmx-users] Different results from identical tpr after MD

Thanks for your valuable suggestions. I am totally agree with your views. On Fri, Apr 6, 2012 at 00:11, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my

Re: [gmx-users] Different results from identical tpr after MD

On 6/04/2012 3:53 PM, bipin singh wrote: Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such