[gmx-users] Gromacs tabulated potentials for CG models

[Sudip Das]

Dear All,

Please find two more files in the attachment which I forgot to attach in my
previous mail in this thread.

Regards,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Tue, Jun 19, 2018 at 2:27 PM, Sudip Das <das.sudip37 at gmail.com> wrote:

> Dear All,
>
> I want to use Gromacs to simulate my coarse-grain model. Our group
> developed the coarse-grain parameters for the system of interest. The
> non-bonded parameters are having a different potential form for different
> pairs. I came across a documentation (http://www.gromacs.org/@api/
> deki/files/94/=gromacs_nb.pdf)
> where we can use a different potential form in a simulation. Here I am
> attaching the itp file.
>
> While I am running the NVT equilibration on the system using 4 cores, the
> simulation is running fine, but when I am using the same configuration on
> more than 4 cores, I am getting an error saying that,
>
> Fatal error:
> 1 of the 35535 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for
> pairs and tabulated bonds also see option -ddcheck
>
> I want to know how to rectify this problem.
>
> Eagerly, waiting for your reply.
>
> Thanks in advanced.
>
> Regards,
> Sudip Das
>
> PhD Student
> C/o. Prof. S. Balasubramanian
> Molecular Simulations Lab
> Chemistry and Physics of Materials Unit (CPMU)
> Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
> Bangalore, India
> ‌
>