>Send gmx-users mailing list submissions to > gmx-users@gromacs.org > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users >or, via email, send a message with subject or body 'help' to > [EMAIL PROTECTED] > >You can reach the person managing the list at > [EMAIL PROTECTED] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of gmx-users digest..." > > >Today's Topics: > > 1. RMSD VS. parallel simulation (DeChang Li) > 2. Re: RMSD VS. parallel simulation (Mark Abraham) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Sat, 5 Apr 2008 11:48:15 +0800 >From: "DeChang Li" <[EMAIL PROTECTED]> >Subject: [gmx-users] RMSD VS. parallel simulation >To: gmx-users@gromacs.org >Message-ID: > <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=ISO-8859-1 > >Dear all, > > I used Gromacs-3.3.1 to simulate a small protein in water. >I have used 2 and 16 CPUs to do the simulation respectively. But >I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs >simulation and 0.20 nm in the 16 CPUs one. Are these differences >reasonable? > In the 16 CPUs simulation, the RMSD of protein at t=0 was about >0.1 nm, why not equal to zero? I used the initial structure for the >least squares fit. > > > > >Best regards, >2008-4-5 > > >========================================= >Dechang Li, PhD Candidate >Department of Engineering Mechanics >Tsinghua University >Beijing 100084 >PR China > >Tel: +86-10-62773779(O) >Email: [EMAIL PROTECTED] >========================================= > > >------------------------------ > >Message: 2 >Date: Sat, 05 Apr 2008 14:02:29 +1000 >From: Mark Abraham <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] RMSD VS. parallel simulation >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >DeChang Li wrote: >> Dear all, >> >> I used Gromacs-3.3.1 to simulate a small protein in water. >> I have used 2 and 16 CPUs to do the simulation respectively. But >> I got the RMSD of the protein equilibrated to 0.15 nm in the 2 CPUs >> simulation and 0.20 nm in the 16 CPUs one. Are these differences >> reasonable? > >MD allows you to observe an ensemble (usually at or approaching >equilibrium) over time. Any single point of that time isn't any more >significant than any other. So you should expect any pair of points in >different simulations (which had their velocities generated with >different random numbers, right?) to generally give different values for >observables, and for that not to mean anything much. Distributions of >observables over long enough periods of time should be the same, however.
I have done the two simulation last 1 ns long. For the last 500ps, the RMSD of the protein is 0.21nm (0.016nm) in the 16 CPUs simulation, but 0.15nm (0.011nm) in the 2 CPUs simulaiton, respectively. (The value in parentheses reflects the standard deviation). I think at the last 500ps the system should be equilibrium. Why the RMSD so different? Does it mean I should simulate much longer? > >> In the 16 CPUs simulation, the RMSD of protein at t=0 was about >> 0.1 nm, why not equal to zero? I used the initial structure for the >> least squares fit. > >If you've done an equilibration or EM, the structure can have changed >during that. I mean the initial structure is the structure I used to generate the .tpr file for mdrun_mpi. >Mark > > >------------------------------ > >_______________________________________________ >gmx-users mailing list >gmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! > >End of gmx-users Digest, Vol 48, Issue 12 >***************************************** = = = = = = = = = = = = = = = = = = = = 致 礼! Dechang Li [EMAIL PROTECTED] 2008-04-05
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