Hi TSjerk, Thanks for the explaination. It is appreciated.
Belquis > Hi Belquis, > > Just some background on the issue. The reason that your solution > worked, and therefore the failure of your first procedure, is that in > the second case the frame at t=10ns was modified using the frame at > t=10-timestep ns as reference, whereas the modification in the first > case was done using t=0ns as the reference. In 10 ns a lot of > translation and rotation happens, making the routine for removing > jumps over periodic boundaries inadequate. > > Cheers, > > Tsjerk > > On 6/21/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: >> Hi Tsjerk, >> >> Thank you for replying. I did give it a reference structure where the >> two >> parts are together. I solved the problem finally! >> I had a 10ns simulation before that and I used -pbc nojump on the >> original >> trjactory and it worked fine..but when I did it for the extra 10 ns i >> ran, >> it didnt work out. It only worked out when I joined the two 10ns >> original >> trjactories and used -pbc nojump. >> >> Thank you >> >> Belquis >> >> >> >> > Hi Belquis, >> > >> > You have to give trjconv a reference structure in which the parts are >> > together and which is close to the starting configuration. This has >> > been mentioned on the list before. For more information, search the >> > archives on trjconv and/or periodic boundary conditions (and possibly >> > my name). >> > >> > Cheers, >> > >> > Tsjerk >> > >> > On 6/21/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: >> >> Hello all, >> >> >> >> I have tried using trjconv -pbc(all options) to get a continuous >> >> trjactoary visulations on VMD. I am modeling an 11 residue receptor >> >> antiparellel to itself and one of the receptor strand jumps outside >> the >> >> box sometimes. >> >> >> >> I have used search to solve the problem but everthing i tried didnt >> >> work >> >> and the -pbc just makes it worse. >> >> >> >> I tried using the -pbc nojump alone and this made my two receptor >> >> strands >> >> away from each other all the way (one inside and one outside the >> box). >> >> However i want them to be close together since they are hydrogen >> >> bonded. >> >> >> >> I have also tried: nojump then whole; whole then nojump and they >> make >> >> the >> >> receptor just fly around or pieces of it stretch. >> >> >> >> anyhelp is appreciated. >> >> >> >> Belquis >> >> >> >> _______________________________________________ >> >> gmx-users mailing list gmx-users@gromacs.org >> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> >> >> > >> > >> > -- >> > 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 >> > _______________________________________________ >> > gmx-users mailing list gmx-users@gromacs.org >> > http://www.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > >> > >> > >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > > -- > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
