Date: Tue, 11 Mar 2014 06:37:38 +0000 (GMT)
Dear Dan, Jason, and David, Thanks for your prompt response. Well, I keep trying those commands that you suggested but I don't get of what I want. I keep seeing the layers of water like climbing a ladder. The same goes to those lipids layers as well. As to understand what is going on during the processing of the trajectories, I would like to investigate these commands one bye one systematically. Start from first I tried to use the command ptraj topology.top << EOF trajin abcdef01.traj trajin abcdef012traj .. .. .. unwrap :1-1214 trajout ABCD.nc netcdf EOF I notice some of the water molecules become so big in size compare to the other water molecules. I have attached a snapshot of that for your view. It is really surprising me. Why few water molecules having some length bonds? I think this is the one shows very long lines during the run of the trajectory in VMD. Please advice why this happens if possible. Thank you. Vijay note: I repost this message with reduced picture size. Vijay Manickam Achari (Phd Student c/o Prof Rauzah Hashim) Chemistry Department, University of Malaya, Malaysia vjramana.gmail.com On Tuesday, 11 March 2014, 13:50, Vijay Manickam Achari <vjrajamany.yahoo.com> wrote: Dear Dan, Jason, and David, Thanks for your prompt response. Well, I keep trying those commands that you suggested but I don't get of what I want. I keep seeing the layers of water like climbing a ladder. The same goes to those lipids layers as well. As to understand what is going on during the processing of the trajectories, I would like to investigate these commands one bye one systematically. Start from first I tried to use the command ptraj topology.top << EOF trajin abcdef01.traj trajin abcdef012traj .. .. .. unwrap :1-1214 trajout ABCD.nc netcdf EOF I notice some of the water molecules become so big in size compare to the other water molecules. I have attached a snapshot of that for your view. It is really surprising me. Why few water molecules having some length bonds? I think this is the one shows very long lines during the run of the trajectory in VMD. Please advice why this happens if possible. Thank you. Vijay Vijay Manickam Achari (Phd Student c/o Prof Rauzah Hashim) Chemistry Department, University of Malaya, Malaysia vjramana.gmail.com On Tuesday, 11 March 2014, 0:45, Jason Swails <jason.swails.gmail.com> wrote: On Mon, Mar 10, 2014 at 11:57 AM, Thomas Cheatham <tec3.utah.edu> wrote: > > > > If I could, I would RMS fit to the first frame the > > > anchor, but RMSd rotates the box so this will kill imaging. Ideally, I > > > would figure out how much in X,Y, and Z the anchor has moved and then > > > translate back or do an RMS fit without rotation (which I do not think > is > > > possible at present... > > > > There is indeed a "norotate" option to the rmsd command in recent > versions > > of cpptraj.... > > D'oh. Maybe I should read our manual! Then, what I would do is pick a > lipid residue of interest, rms fit to that with norotate to the first > frame, and then autoimage. Dan/Jason, you can let us know if this will > not work. --tec3 > I thought a simple "center" command would work (since that should translate that lipid in every frame back to the origin) followed by an "image origin center" which would image around that point. I suggested only a single atom on the tail-end of the lipid just to drop the origin as close to the 'center' of the bilayer as possible, but for a large box the COM of a lipid and the center of the bilayer is probably close enough. That said, I don't see why a rms fit with norotate would fail to work... The autoimage command may still be the best approach since that should handle translating a particular lipid (in this case the first lipid molecule) to the center of the box in every frame and imaging the rest of the bilayer around it. The OP can experiment with the different approaches to see which one fits best... All the best, Jason -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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(image/png attachment: water-mol-get-bigger.png)
