[gmx-users] Re: RMSD VS. parallel simulation

Dechang Li li.dc06 at gmail.com
Sat Apr 5 12:29:05 CEST 2008


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>Today's Topics:
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>   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" <li.dc06 at gmail.com>
>Subject: [gmx-users] RMSD VS. parallel simulation
>To: gmx-users at gromacs.org
>Message-ID:
>	<bbfc6b070804042048s297a545fie0d4122ae70d19a3 at mail.gmail.com>
>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: lidc02 at mails.tsinghua.edu.cn
>=========================================
>
>
>------------------------------
>
>Message: 2
>Date: Sat, 05 Apr 2008 14:02:29 +1000
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>Subject: Re: [gmx-users] RMSD VS. parallel simulation
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <47F6F9D5.8090305 at anu.edu.au>
>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
>
>
>------------------------------
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>End of gmx-users Digest, Vol 48, Issue 12
>*****************************************

= = = = = = = = = = = = = = = = = = = =
			

        致
礼!
 
				 
        Dechang Li
        Li.DC06 at gmail.com
          2008-04-05



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