[gmx-users] water molecule cannot be settled during minimization!!!!

Vytautas Rakeviius vytautas1987 at yahoo.com
Tue Nov 7 13:36:04 CET 2017

Investigate same water molecule mentioned in error in vmd or such program likely it is in close contact to other molecule.You can move it manually by altering coordinates in gro text file into more realistic starting position.Or probably even better if you redo your solvatation again (with different parameters?).

    On Monday, November 6, 2017, 7:18:18 AM GMT+2, Seera Suryanarayana <palusoori at gmail.com> wrote:  
 Dear gromacs users

I am trying to simulate one protein with 180 residues. During energy
minimization I got the falling error.

Fatal error:

step 26: Water molecule starting at atom 28787 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

I have reduced the em step size from 0.01 to 0.02  as I got this suggestion
from archives. I  still have the same problem. I request you to give a
suggestion how to resolve it.

Thanks in advance
Graduate student
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