Re: [gmx-users] minimization of particular residue/atom
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.comwrote: 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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] minimization of particular residue/atom
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.comwrote: 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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] minimization of particular residue/atom
On Wed, May 1, 2013 at 4:20 PM, gromacs query gromacsqu...@gmail.comwrote: 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 listgmx-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 listgmx-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
