Re: [gmx-users] minimization of particular residue/atom

2013-05-02 Thread gromacs query
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,

Re: [gmx-users] minimization of particular residue/atom

2013-05-02 Thread Mark Abraham
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 =

[gmx-users] minimization of particular residue/atom

2013-05-01 Thread gromacs query
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) I removed the full lipid residue having

Re: [gmx-users] minimization of particular residue/atom

2013-05-01 Thread Mark Abraham
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 =