[gmx-users] temperature shooting up

[Cherry Y. Yates]

Dear Mark,

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? 

Many thanks,

Cherry







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 
temperature coupling.

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.

Mark
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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 
http://mail.yahoo.com 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20061108/ad4f2dd1/attachment.html>