From: Alessandro Cembran (cembran_at_chem.umn.edu)
Date: Wed Jun 27 2007 - 09:08:32 CDT
I think his concern is more than just getting the right rmsd. I had a
similar concern in the past, when my goal was trying to get an estimate
of the diffusion coefficient of a protein in a lipid membrane. What I
found is that the entire membrane together with the protein was drifting
in a given direction, so to get rid of this bias I had to subtract the
COM of the entire system (I also found in literature that there are
people that even remove the COM for each layer independently, see Edholm
J.C.P. 2001, 115, 4938 or Lyubartsev J.P.C.B 2006, 110, 14362). In order
to do this one had to write some script to unwrap the coordinates from
the PBC, if wrapall is specified.
Furthermore I noticed a weird behavior, in my first simulations I was
using "ComMotion no", meaning that every time I restarted my simulation
the total velocity of the system was reset to zero. This caused an
artificial oscillation to show up in the drifting of the system, clearly
at the same frequency (a few ns) with which I was restarting my
simulations. Since then I turned it off and I am simulating with
"ComMotion yes" and I am removing the total box drifting COM afterwards.
I'd also like to hear some comments about this.
Alessandro
Cesar Luis Avila wrote:
> To get rid of the diffusion why don't you just align the C alpha atoms
> of your protein between frames before calculating the rmsd.
>
> Ilya Chorny escribió:
>> Hello All,
>>
>> After analyzing my trajectories of a large protein in a membrane, I
>> noticed the my protein shifts about 3 A after about 10 ns. Would
>> one expect diffusion on this time scale? Taking a diffusion constant
>> of about 10^-8 cm^2/s the conversion into MD units is .1A^2/ns (if I
>> did the math right), thus 3 A seems a bit much. Any thoughts?
>>
>> I am also working with a manic cluster which kills my jobs every so
>> often, at which point I restart the trajectories with new initial
>> veloocites. Could restarting with new initial velocities cause a
>> shift/diffusion.
>>
>> Finally, I do not zero the CM motion of the system. Does that mean I
>> have a non-zero CM velovity, and thus I should expect the system to
>> drift as a whole?
>>
>> Thanks,
>>
>> Ilya
>>
>>
>> --
>> Ilya Chorny Ph.D.
>
-- Alessandro Cembran,PhD Post Doctoral Associate Mailing Address: Univ. of Minnesota, Dept. of Chemistry G2, 139 Smith Hall 207 Pleasant St SE Minneapolis, MN 55455-0431 Office: Univ. of Minnesota, Walter Library 117 Pleasant St SE, Room 473 Phone: +1 612-624-4617 E-mail: cembran_at_chem.umn.edu
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