[gmx-users] AMP_simulation

Dallas Warren dallas.warren at monash.edu
Tue May 29 04:24:12 CEST 2018

The ATB generator does a reasonable job, but for some reason it gets
some things wrong.  If you can look at that topology, identify the
problematic parts of it, see if that is consistent with the
forcefield, and then if not adjust the parameters.  Particularly I
have found that some angles are way too large, giving fast moving bond
angles, which then become unstable.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 24 May 2018 at 22:01,  <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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