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 [email protected] >> 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 [email protected] > 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 [email protected] 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
