[gmx-users] nsgrid error

[Xavier Periole]

Hello,

1) I guess that before running at NVE you equilibrated your system to 
get the right temperature.
Generaly you can get that in some 20-50 ps run in NVT (even NPT). The 
idea is to control the
temperature till you get the equilibrium Kenetics/Potential energies. 
When you get to the equilibrium
you can let the system go without rescaling the temperature but you 
still have to check that there is
no drift of temperature. What is surely what is happening to your system 
anyways.

2) I bet you that if you check the temperature of your system you'll see 
that it is not the one you
want. It is likely to increase and that is probably why you molecules 
can not be settled. Too much
derive from the correct configuration. That is due to the 
non-conservation of the energy of your
Hello,

1) I guess that before running at NVE you equilibrated your system to 
get the right temperature.
Generaly you can get that in some 20-50 ps run in NVT (even NPT). The 
idea is to control the
temperature till you get the equilibrium Kinetics/Potential energies. 
When you get to the equilibrium
you can let the system go without rescaling the temperature but you 
still have to check that there is
no drift of temperature. What is surely what is happening to your system 
anyways.

2) I bet you that if you check the temperature of your system you'll see 
that it is not the one you
want. It is likely to increase and that is probably why you molecules 
can not be settled. Too much
derive from the correct configuration. That is due to the 
non-conservation of the energy of your
system in the NVE which always results in an increase of the temperature 
(kinetics energy).
The non-conservation of the energy is due (in your case, that what I 
would guess) to the use of
straight cut-offs, which can be fixed by the use of switch or shift 
functions that make (partially)
sure that when particules get in and out of your cutoff there is no 
dramatic change in the interaction
energy (more precisely the forces), which again results in an increase 
of the kinetics energy
(temperature).

The solution if you want to keep working in NVE: use a good smoothing 
function of your energy
(forces). I would recommand the force-shift.

Hope it helps
XAvier

-- 
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   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   
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