[gmx-users] molecular dynamics problems

Xavier Periole x.periole at chem.rug.nl
Tue Jul 20 13:23:08 CEST 2004

vlad.chindea at pharmatech.ro wrote:

>Dear Xavier
>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 
simulations is
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 
the temperature
your are comparing. It is impossible to have a solvent at 300K and 
"localy" 200K.
If you actaully have the correct definition of the local temperature. 
Check the Sybyl
manual !!

>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
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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