[gmx-users] About Warning in grompp
jalemkul at vt.edu
Sun Sep 23 13:45:55 CEST 2012
On 9/23/12 4:17 AM, vidhya sankar wrote:
> Dear Gromacs users
> i am doing NPT Eqlibration for a cyclic peptide
> When I run grompp I have got Warning as follows
> WARNING 1 [file 2KDQ3.top, line 1137]:
> The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H has
> an estimated oscillational period of 1.0e-02 ps, which is less than 5
> times the time step of 2.0e-03 ps.
> Maybe you forgot to change the constraints mdp option.
> How to Rectify this Warning?
The output suggests one way (use of constraints). Otherwise shorten dt if you
don't want to use constraints.
> If i Neglect using -maxwarn 1 option then have got Segmentation Fault during mdrun
Overriding warnings is generally a bad idea. grompp is telling you that you
have a physically unstable model, so the fact that mdrun crashed is unsurprising.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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