[gmx-users] Hydroxyl bonds rotating too much

Juan José Galano Frutos juanjogf at gmail.com
Tue May 16 13:03:12 CEST 2017

Hi there:

I am simulating a protein which include as a cofactor a molecule bearing
some hydroxyl groups. The system is crashing from the begining of the
equilibration step (after the following steps: vaccuum minimization,
solvating, neutralizing, minimization, heating) due to -in all the
replicas- to hydroxyl bonds that steadily rotated more than 60 and even 90
I checked the structures and the systems looking for either water or
protein parts in so close contact with this hydroxyl groups, but it was not
the case. Then I proceeded to re-minimize again the systems after the
heating step and afterward to relaunch the equilibration step, but again
the same happened. I also checked the topology file of this cofactor but
all seems to be fine, I mean charges.
Then, what could be happening? Is it common this behaviour in hydroxyl
groups?Any help please....



Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)

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