[gmx-users] molecular dynamics problems
x.periole at chem.rug.nl
Tue Jul 20 13:23:08 CEST 2004
vlad.chindea at pharmatech.ro wrote:
>First of all, if I am not wrong I know that decreasing thermostat coupling
>constant allow faster equilibration of the system. Default value in Sybyl
>is also 100fs but when I saw that local temp. are not what they should
>be,I decrease the value, in order to heat more the system.
It is not a faster equilibration ! it is a way to compensate the fact
that your system is
doing bad. Decreasing the temperature coupling constrains your system a
lot. It is
not really free to move the way it would with a coupling constant 0.1ps.
>Actually I have to run in NPT, but when I saw that I cannot achieve
>equilibrium, and the volume keeps increasing (I used again 20fs coupling
>constant with scaled velocities, maybe this is the culprit?) ruining my
>density, I switched to NVT, to have a looksee.
If your volume keep increasing that means that with the protocol (conf,
pressure coupling, temp coupling, equilbration ...) the system needs to
Perhaps it is ok. How big is the expention ? What are the initial and
final densities ?
anyways 20 ps equilibration is not much is the starting point of your
far from equilibrium.
Iwould check the density and how bad (or good) your volume is doing.
>Local temp. are mesured by Sybyl by selecting molecules of interest,
>(probably by the same algorithm as total temp.) so I choose the whole
>solvent molecules and while reported temp. for the system was 300K for
>solvent was only 200K.
You agree that this not likely to be correct !!! Something i wrong in
your are comparing. It is impossible to have a solvent at 300K and
If you actaully have the correct definition of the local temperature.
Check the Sybyl
>When I measured the temp. of the solute molecule (only 41 atoms from 4850
>of the whole system)it was even lower then solvent temp., which led me to
>belive that I have a 'hot solvent, cold solute situation' From your
>experience what is the normal variation of local temp.(compared to total
>temp.) in a well behaved simulation?
A solvent at 200 K and a solute at <200K and the full system 300K !!!!
is definitely wrong.
>Velocities were assigned randomly at the begining of the simulation.
>Bug in the software was more like a rethorical question, I know that most
>probably I am doing something wrong but i cannot figure out what.
>What would be the normal course that you would employ for a simulation of
>this kind (solute in water, equilibrated at 300K in NPT) ?
Check the density/volume expension, check the definitions of the
temperatures you are
comparing, and think about using another sofware !!
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
9747 AG Groningen
email: x.periole at chem.rug.nl
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