Thanks Tsjerk I referred the mail about the broken molecules but there the problem is i think somewhat different. in that case broken molecules are coming becasue of the PBC . since PBC is being used that is why some part of the molecule is coming from the other side of box and its looking as if protein is broken
but in my case i think the situation is different, first of all i have not still started using the PBC in the simulation and my full molecule (broken molecule) is right in the center of the box. moreover i am getting this problem before starting any simulation. till i did some simulation in vaccum before adding ions , it went fine there and then while shifting to the water simulation i added ions and right after adding the ions my molecule is getting broken. Thanks With Regards Gurpreet 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Gurpreet, I didn't ask whether you used PBC, I suggested it was due to PBC. Check the archives for "broken molecules" and such. Tsjerk On 7/16/07, gurpreet singh <[EMAIL PROTECTED]> wrote: > Thanks Tsjerk for you reply > i did not get your point . i think you are asking me whether i used PBC or > not , so i want to tell you that the .tpr file which i used for genion > command was created without using PBC. > > but will it make any difference ? > > Thanks > With Regards > Gurpreet > > On 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED] > wrote: > > > > Gurpreet, > > > > > my system was going fine at that time but when i used the genion > command to > > > add ions , i found that my protein was broken into parts. > > > what could be the reason for this ? > > > > PBC? > > > > > While running the genion it usually asked for the group into which we > want > > > to add the ions so i have checked with both the SOL group and OTH group > > > seperatly , in both the cases ions were replacing the solvent molecules. > Is > > > their any way by which we can add ions without replacing any solvent > > > molecules ? > > > > No, there's no space to put them. > > Well, you could try to squeeze them in here or there manually, and > > perform energy minimization... > > > > Cheers, > > > > Tsjerk > > > > > > -- > > 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
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