[gmx-users] Harmonic potential

M.Naser mn2 at hw.ac.uk
Fri Dec 31 13:07:21 CET 2004

Hi Michael,

Thank you very much for your sggestions.

With best reagrads,

>> > Thank you very much for your response.I have a protein in a water slab
>> > which is placed in a vacuume. When I ran 1 ns run the water drifted
>> away
>> > from the slap into the vacumme which I did not want. I have wondering
>> > whether I could apply harmonic potential in the water slab to stop
>> > drifting water when I go for longer run. Could you please advise me
>> how to
>> > apply harmonic potential in water slab or anyother way I can tackle
>> the
>> > problem?
>> Sorry, that's not implemented, the only thing you could try is position
>> restraints in the Z dimension for the outer layer of water
> as a workaround you could use umbrella sampling as implemented
> in the pull code, this comes basically down to applying a harmonic
> potential to a group of your choice. You can ignore the output
> in the pull.pdo ...
> However, if your water slab is thick enough it should not disintegrate
> at all, and if occasionally one or a few single water molecules
> drift away from your slab that shouldn't much of a difference ...
> If the slab does disintegrate entirely then you should check your
> system and settings because something else might go wrong there.
> michael
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