[gmx-users] About Warning in grompp

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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