[gmx-users] question about dynamics

[Shuangxing Dai]

Thanks for the help. 
The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat.
Do you have any idea of this information?

Thanks,
Shuangxing Dai

On Jul 12, 2010, at 15:43, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:

> 
> 
> Shuangxing Dai wrote:
>> Hi, all:
>>    I am studying thermal expansion of bulk crystal solid. I want to reach the state with 300K in temperature and 1 bar pressure.  I am not sure whether my procedure is correct or not.
>>    First I run energy minimization, then a constant volume for temperature coupling ( integrator is sd), then run with Berendson for anisotropic pressure coupling for 50 ps, then run anisotropic pressure coupling using Panello-Rahman for 10 ps, finally a constant volume step for production for 10 ps.
>>    I do not know whether this procedure is correct or not.  Also, since for my small system, fluctuation is very large, so is there any way to reach the state ( 300K and 1 bar) and the system is fully in equilibrium?
> 
> The timeframes you're using are extremely short.  I'd suspect that it would be hard to get any system, especially a small one prone to large fluctuations, in an equilibrium state in 70 ps total.  Simple equilibration of a protein in water is typically done for no less than 100 ps per ensemble.
> 
>>    Also, I got a question about the ,mdp file options. When I use md integrator, with Nose-Hover for temperature coupling and Panello-Rahman pressure coupling, there is no error information. When I change and use Berendson for pressure coupling, there is error information and does not work.
> 
> Well, what's the error?  This kind of description will get you no useful advice.

The error information is: Using Berendsen pressure coupling invalidates the true ensemble for the thermostat.

> 
> -Justin
> 
>>   Anyone have idea about these? Thanks in advance.
>> Thanks,
>> Shuangxing Dai
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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