[gmx-users] MD of methanol

[Mark Abraham]

Hi,


If you have an .itp then you have no need of editing an .rtp file that is
only used by pdb2gmx. That the simulation is unstable is unrelated, and we
don't have enough information to suggest why. Please do make sure you
understand how the pieces work, eg by trying the tutorials if you have not
already done so.

Mark

On Tue, Feb 20, 2018, 07:52 Adriano Santana Sanchez <
adriano.santanasanchez at kaust.edu.sa> wrote:

> Hi,
>
> I am trying to run energy minimization of a methanol molecule.
>
> I have a .pdb file of a single MeOH molecule and a  methanol.itp
> file with parameters for the OPLSAA force field.
>
> I have added an entry for this '.itp' into 'aminoacids.rtp' putting [atoms]
> [bonds].
>
> I can create a topology file this way but the simulations are unstable.
> What am I missing?.
>
> Thanks,
> Adriano
>
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