That procedure can work. That it works in your case surprises me a little. :-)
Mark On Thu, May 2, 2013 at 11:25 AM, gromacs query <gromacsqu...@gmail.com>wrote: > Dear Mark, > > I found a simple(est) fix to this problem. Say in my case I was getting > error inf on atom 4281 ( Maximum force = inf on atom 4281) > > What I did: In gro file for atom number 4281 I edited one of its > coordinate just 0.1nm that is 1 Angs e.g. 6.518 to 6.618 (I did for x, but > can be y or z). So mdrun was complaining one by one and I edited in all > three such x coordinates for three atoms. finally I was able to achieve > convergence. > > I believe moving just 0.1 nm minimization will take care of correct > lengths. May be if its not the correct way; please suggest. > > regards, > > > On Thu, May 2, 2013 at 12:50 AM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > On Wed, May 1, 2013 at 4:20 PM, gromacs query <gromacsqu...@gmail.com > > >wrote: > > > > > Dear All, > > > > > > I am using Charmm gui built membrane (120 x 2). But during > minimization I > > > was getting error. > > > > > > Potential Energy = 4.6809051e+19 > > > Maximum force = inf on atom 4281 > > > Norm of force = inf > > > > > > > > > (inf means? means infinite/NAN) > > > > > > > All the above means your system is > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up > > > > I removed the full lipid residue having atom number 4281. I was again > > > getting error representing some other atoms so finally I removed three > > > lipid residues. Doing this I was able to complete convergence. > > > > > > I have two queries: > > > > > > 1) As I have removed three residues from Charmm gui membrane, does this > > > affect final results? Although I will be doing MD for membrane first. > > > > > > > Maybe. We don't know whether the membrane was built wrongly, or you > > post-processed the coordinate file wrongly, or whether you need all the > > lipid molecules to achieve the right density, or... > > > > > > > 2) Also is there any way so that particular atoms can be minimized or > > > ''touched'' ? Here in this case I removed three lipid residues but this > > > will not be good say in case of proteins. Just as a analogy if this > > problem > > > arises in AMBER (rather I faced such problem many times) I can use > xleap > > > and can move atom a little and relax it particularly by selecting it , > so > > > that later if use the edited structure I get convergence properly > without > > > error. > > > > > > > You can only do that by moving the coordinates by hand in the coordinate > > file before you give it to grompp. Your PE above is so large that this is > > not the right approach to fix the problem. I would guess your periodic > box > > is not the one you were intended to use. > > > > Mark > > > > > > > > > > regards, > > > Jio > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > > 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 gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > 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 gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
