[gmx-users] temperature shooting up
Cherry Y. Yates
yappik4050 at yahoo.com
Wed Nov 8 09:20:30 CET 2006
Thanks for your help. Actually I did separate runs for flexible and rigid models, and didn't use the equilibrated flexible structure to start with rigid model calculations. But the starting configurations are the same. So do you mean I need to reduce the T-coupling time? If the initial water geometry is not the same as the rigid model, does the program will "enforce" that geometry for water molecules, or to "relax" water molecure towards it?
Mark Abraham <Mark.Abraham at anu.edu.au> wrote: Cherry Y. Yates wrote:
> Dear Mark,
> Thanks for your help, I followed you instruction, and I can get stable
> temperature after I remove the temperature coupling. In this case I used
> the flexible spc itp file. However if I use a rigid spc.itp, after
> remveing the temperature coupling, the system temperature is shooting up
> from 300K to thousands degree, the total energy is going up also instead
> of fluctuating. I attached both the itp files and grompp.mdp files. Let
> me know what could be wrong. It is really wired to me.
The change in the model physics from flexible to rigid is severe one -
almost all of the water molecules won't fit the rigid geometry, and will
thus be in a high-potential-energy state. If the constraint-enforcing
algorithm conserves energy, then that potential energy has to be
converted to kinetic energy. Then if the simulation lacks temperature
coupling, it is at constant energy and the temperature will be
necessarily high. Actually you say you observe rising energy - this is
probably because your timestep is too large to conserve energy at this
very high temperature (and thus atomic velocity).
So the take-home lesson is not to do two perturbations of your model
physics at one time. If you really want to start with a flexible water
model with temperature regulation and end up with rigid water model at
without temperature regulation, do the water transition with temperature
coupling still on to give the energy somewhere to flow - to the external
bath. I expect you'd need a short temperature coupling constant to make
this work in practice. Once that's stable, *now* try taking off
This suggests the question, why you'd want to do this flexible-rigid
transition in an equilibration? It would be simpler to start in the
rigid domain, and to do energy minimization to correct any geometries
before starting MD simulations.
gmx-users mailing list gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users