[gmx-users] Not able to continue with Equilibration

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 29 17:25:36 CEST 2012

francesca vitalini wrote:
> Hallo Felix,
> thank you for your answer. I tried the constraints = h-bonds but no
> change in the output. If I look at the step.pdb file that is produced
> after the running I have some strange outcome. For example some of my
> atoms are not recognized as part of my protein any more and my
> structure is destroied. Am I using some strange parameters for nvt
> without realizing it? I've started from the mdp file provided by the
> lysozyme tutorial non the Gromacs webpage.

Yes, some of your parameters are very strange:

> rlist           = 3.0           ; short-range neighborlist cutoff (in nm)
> rcoulomb        = 3.0           ; short-range electrostatic cutoff (in nm)
> rvdw            = 3.0           ; short-range van der Waals cutoff (in nm)

None of the force fields in Gromacs are parameterized to use such values.  Your 
crash could be due to the fact that you're breaking the underlying physics.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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