[gmx-users] Error in NPT simulation

[Justin Lemkul]

On 5/29/18 3:11 PM, Nagasree Garapati wrote:
> Dear all
>
>
> I am getting following error while running NPT simulation.
>
> I did energy minimization and NVT simulations, which ran successfully but when I proceed to NPT simulation, I am getting below error.
>
>
> Step 142, time 0.284 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms -nan, max 0.003869 (between atoms 33 and 76)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
> Segmentation fault (core dumped)
>
>
> Not sure, what could be the reason for error.
>
> Any thoughts ?

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

If you need more detailed guidance, you'll have to be more specific 
about what you're doing. There are any number of things that could be 
going wrong (inadequate equilibration, inappropriate .mdp settings, 
unstable custom topology, etc).

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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