On Mon, Jan 30, 2012 at 1:46 PM, Justin A. Lemkul <[email protected]> wrote:
> > > Steven Neumann wrote: > > >> >> On Mon, Jan 30, 2012 at 12:16 PM, Mark Abraham >> <[email protected]<mailto: >> [email protected].**au <[email protected]>>> wrote: >> >> On 30/01/2012 8:43 PM, Steven Neumann wrote: >> >>> Dear Gmx Users, >>> I run the simulation of protein with 10 ligands (200 ns). In >>> total >>> I should have total of 4000 frames as I set up: >>> >>> nsteps = 100000000 >>> >>> dt = 0.002 >>> >>> nstxout = 25000 >>> >>> >> ... iff the simulation completed successfully. >> >> >> I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump >>> >>> The trajectory which I read in VMD has 3008 frames and my ligands >>> completely disappear after 8 frame (They are not in PBC windows >>> which I checked in Graphics -> Graphical Representation -> Periodic) >>> >>> >> Your choice of trjconv workflow demands that the protein be allowed >> to diffuse away. What VMD makes of that is not really of consequence >> to discuss here. Perhaps you can design a better trjconv workflow, >> as here >> http://www.gromacs.org/**Documentation/Terminology/** >> Periodic_Boundary_Conditions<http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions> >> >> >> Thank you. I managed to fix it using: >> trjconv -f md.trr -o md1000.xtc -skip 4 (1000 frames instead of 4000) >> Then accoring to the workflow (PBC) I used: >> >> trjconv -f md1000.xtc -s md.tpr -pbc mol -o mdmol.xtc >> trjconv -f mdmol.xtc -s md.tpr -center -o mdCENTER.xtc (Center on a >> protein, output - System) >> >> trjconv -f mdCENTER.xtc -s md.tpr -fit rot+trans -o mdFit.xtc (Protein, >> output - System) >> >> >> However, all ligands jump rapidly >> >> around the protein till the time they bind to the protein surface (and >> the begining they were randomly placed around the protein) one by one. At >> the end when all of them stacked on my protein everything is ok. Will you >> suggest something? >> >> >> > > Is this unusual? It sounds like the molecules diffuse around until they > bind to the protein. You're centering on the protein and then fitting its > translation and rotation; everything else will be processed relative to > those criteria. > > -Justin > > Sorry, I did not clarify it properly. What is unusual is that my ligands (until they bind) jump to its periodic images. It is a speed light diffusion :) Any suggestions? > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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