On Thu, 27 Dec 2007 08:55:03 +0100
"Tsjerk Wassenaar" <[EMAIL PROTECTED]> wrote:
Hi,
Just to add my 5 cEUR. The flying ice cube will be avoided using linear comm
removal on the whole system (default), which will retain diffusion of the
peptide in the solvent.
Thanks Tsjerk for clarifying my quickanddurty statement. Removing the COM
motion of the whole system is fine, my concern was to do it separately on
the solvent and peptide.
The peaks you see in the comm I guess are due to the
update of the neighbour list (every ten steps?). This will change the system
a bit more than usually, causing the peptide to suddenly see different
interacting particles.
Cheers,
Tsjerk
On 12/26/07, Xavier Periole <[EMAIL PROTECTED]> wrote:
On Wed, 26 Dec 2007 09:01:22 +0100
David van der Spoel <[EMAIL PROTECTED]> wrote:
> Li Qiang wrote:
>> hi Christian,
>>
>> Thanks for the reply. I have plotted the the rate of center of mass
>> motion and found there are peaks with certain time interval. I think
>> that is not only a visual problem but like fly ice cube problem(not
>> sure). As a comparison, when a large protein is simulated, the
>> rate(velocity) of COM is "constant".
>>
I do not think you want to remove the center of mass motion of your
peptide, and certainly not of your solvent. The diffusion of the peptide
is certainly something you should expect. If it looks like a flying
ice cube that means that there are some parameters that you should
modify in your mdp file.
>> Yes. the default way GROMACS do is system COM removal at each step.
>>
>>
>> how does the program remove this center of mass motion?
>>
> By summing the COM momentum and subtracting it from all atoms.
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax:
+4618511755.
> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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