[gmx-users] minimization of particular residue/atom
gromacsquery at gmail.com
Wed May 1 16:20:53 CEST 2013
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 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.
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
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