[gmx-users] Water molecule can not be settled

[Mark Abraham]

Hi,

Google has some good suggestions for examples for GROMACS mimization in
vacuo. You want no PBC, simple grid and maybe no cutoffs.

EM has no time, so time step is not a relevant concept. The .mdp option
documentation is quite useful...

Mark

On Thu, Jun 30, 2016 at 12:15 PM zeineb SI CHAIB <zeineb-14 at hotmail.com>
wrote:

> Dear Mark,
>
> Thank you very much for your answer.
>
> I'm trying to minimize my protein in vacuo but I'm havig problem to
> undrstand the concept of "in vacuo" so I'm enable to construct an mdp file
> and I can't found valid examples in forums and internet. Could you help me
> with that please?
>
> Also, the "time step of the minimisation is 'emstep', is it correct?
>
> Thank you very much for your help.
>
> Zeineb.
>
>
>
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