Hi, Thanks for the mail. I checked my input structure. I dont have any water along with the protein. Regards, Ragothaman
--- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Ragothaman, > > Also check for isolated water molecules. These can > be a pain, since > they are sort of part of the protein, but are > coupled to the solvent > outside. One common source for > LINCS/water-molecule-can't-be-settled > errors. > > Cheers, > > Tsjerk > > On 5/28/07, Mark Abraham <[EMAIL PROTECTED]> > wrote: > > Ragothaman Yennamalli wrote: > > > Thanks. > > > I do get LINCS warning all the time. I had > removed two > > > water molecule, that seemed too close to where > the > > > LINCS warning came for. And started the > simulation > > > again from the scratch and it stopped as > mentioned in > > > my previous message. > > > > Yup. Go and fix your equilibration regime (copy > something reasonable > > from a published paper or a tutorial). A normal > simulation should have > > no LINCS errors. > > > > Mark > > _______________________________________________ > > 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 > Download prohibited? No problem! To chat from any browser without download, Click Here: http://in.messenger.yahoo.com/webmessengerpromo.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
