Dear Sir,
I have treid to run stfcdiffusion comamnd from cpptraj.
the command I used is as blow.
stfcdiffusion mask :BCM.1 out diffusion_in_XY_plane.dat time 5 avout distance com xy
What I wanto calculate is the diffusion of atom number 1 from residue BCM.
I get the output file with 5 columns with the first one representing time.
But I find difficulty in finding the meaning of those columns wiht the firstone to the time evolution.
Could you explain briefly what the coluns aer reperesenting. Further I get another file called "distance" with only one line data in it.
I want the diffusion along xy plane.
Many thanks in advance.
Regards
Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
On Thursday, 9 January 2014, 0:24, Daniel Roe <daniel.r.roe.gmail.com> wrote:
Hi,
If you want to calculate the mean squared displacement for a 'wrapped'
system, you can first use the 'unwrap' command in cpptraj/ptraj (which is
essentially the reverse of 'image' and will ensure your molecules take
continuous paths), followed by either the 'diffusion' command in
ptraj/cpptraj or the stfcdiffusion command in cpptraj (which is an
alternative to the traditional diffusion command written by Hannes
Loeffler).
Hope this helps,
-Dan
On Wed, Jan 8, 2014 at 12:45 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> Dear SIr,
>
> I am doing bilayer simulation and I would like to calculate MSD (mean
> square displacement) for the lipids in the bilayer.
>
> Since my simulation is quite long (~200ns), I have used flags like ntxo=1,
> iwrap=1, nscm=5000.
>
> In the literature, ( for example J.Chem. Phys., Vol. 115, No. 10, 8
> September 2001) indicated that before the MSD calculation the authors have
> corrected the center-of-mass motion in each layer before calculating. They
> used GROMACS.
>
> Well, since I am using AMBER12, do I still need to do the correction for
> the center-of-mass motion in each layer before calculating the MSD in
> AMBER? If yes how do I do the correction? I could not find anything related
> to this in the manual.
>
> Hope kindly I can get some explanation and help .
> Many thanks in advance.
>
> Regards
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jan 10 2014 - 03:30:03 PST
