[gmx-users] question about dynamics

[Justin A. Lemkul]

Shuangxing Dai wrote:
> 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?
> 

The Berendsen method does not produce a proper ensemble for either temperature 
or pressure.  If you want true NPT, use Parrinello-Rahman.  This is all 
documented there are numerous threads about it in the literature and in the list 
archive.

-Justin

> 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
> 

-- 
========================================

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

========================================