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