[gmx-users] AMP_simulation

RAHUL SURESH drrahulsuresh at gmail.com
Thu May 24 15:13:08 CEST 2018


On Thu, May 24, 2018 at 5:31 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.

Segmentation fault normally occurs for large system with small memory.  You
can write xtc which is a compresssed trajectory file.
Adding time steps to write the file.

> 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.

Lincs warning, as for here without knowing exactly about the system, i
think the error is due to improper minimization.
Minimize properly ir go for double precision method.

> 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".

Yeah, not an issue I guess.

> Thanks
> Nikita Bora

Thanks back

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