[gmx-users] Re: Re: RMSD VS. parallel simulation (Mark Abraham)

[Dechang Li]

gmx-users-request,您好！

	

>>>
>>> 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?
>
>These numbers don't mean anything out of context. Even the most stable
>protein structure of a thousand residues might have an all-atom average
>RMSD of this size. In a decapeptide it might mean there isn't a single
>conformer, or that equilibrium is not yet reached.
>
>>>>   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. 
>
>What were your command lines, choices for groups and outputs? The most
>likely simple explanation is that you haven't done what you think you've
>done :-)

   My command lines:
  
   g_rms -s md.tpr -f md.trr -o rms_protein.xvg -n index.ndx

   choices for groups:
   
    Select group for least squares fit: Protein
    Select group for RMSD calculation:  Protein



 
>Mark
>
>
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