[gmx-users] minimization of particular residue/atom

Mark Abraham mark.j.abraham at gmail.com
Wed May 1 23:50:35 CEST 2013

On Wed, May 1, 2013 at 4:20 PM, gromacs query <gromacsquery at 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

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.


> regards,
> Jio
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