[gmx-users] AMP_simulation

Soham Sarkar soham9038 at gmail.com
Thu May 24 15:09:13 CEST 2018

Try with 1ps time step

On Thu, 24 May 2018, 6:33 pm , <niki24 at tezu.ernet.in> wrote:

> Hello,
> I have tried doing the Molecular dynamics simulation of AMP using the
> Gromos54a7 forcefield.
> ITP parameters for the AMP molecule has been generated using the ATB
> builder. Minimization of the molecule goes on well however while carrying
> out the Nvt theres a segmantation fault resulting in step files.
> Moreover LINCS warning are shown with bonds that rotated more than 30
> degrees. ihave tried changing lincs parameter and also increasing the step
> size, but still simulation crashes.
> Is it suggestible to generate topology for the AMP molecule from the
> available topological parameters of ATP in GROMACS. Or are their any
> source of getting the correct itp paremeters for "AMP".
> Thanks
> Nikita Bora
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