[gmx-users] (no subject)

[Mark Abraham]

Hi,

Off-list Ali sent me a link to his movie - this does indeed show the ligand
diffusing out gradually, rather than "jumping" in a discrete step. Such an
event would be very rare for a lot of bound ligands with a suitable model
physics, so if it's reproducible then you have problems with the model,
somehow.

Mark

On Fri, Apr 15, 2016 at 3:30 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Please see
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> Mark
>
> On Fri, Apr 15, 2016 at 12:22 PM ali osouli <aliosouli.av at gmail.com>
> wrote:
>
>> Dear all
>> My MD run movie shows that my ligand jump out of protein in the early
>> picoseconds of simulation, does anybody knwos which step of my MD should i
>> check?
>> In additon to rutin steps i have included a distance restraint file to
>> topolgy.itp.
>> Best regards Ali
>> --
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>