[gmx-users] NVT + frozen groups

Valentin Gogonea v.gogonea at csuohio.edu
Wed Jul 10 02:01:15 CEST 2002

Thanks again...

I do have to freeze a large part of it. There are more than 1000 amino 
acids (+ water). Perhaps I can apply position restrain for a shell 
around the moving part, but this does not save CPU time. I think that it 
may be better to make the moving part larger.

Thank you again.


On Tuesday, July 9, 2002, at 07:51 PM, Erik Lindahl wrote:

> Valentin Gogonea wrote:
>> Thanks Erik for you quick answer.
>> Does it make sense to make NPT simulations with frozen groups? I mean 
>> if the coordinates of the frozen atoms are not scaled what happen with 
>> the bonds between atoms in the moving part and those in the frozen 
>> part?
>> In a hypothetical situation that the moving region is totally buried 
>> in the frozen one, how does the pressure coupling works? It seems to 
>> me that the box size cannot be adjusted in this case because the 
>> moving part is wrapped in a hard wall. Am I wrong?
> No, it could probably lead to quite strange results, especially if you 
> freeze a large part of the system, so in general it's probably easier 
> to freeze in NVT.
> Are you sure you need to freeze things completely? In most cases it's 
> gentler on the dynamics to just apply position restraints (but even 
> then the coordinates will be constrained to the starting positions, 
> while everything else scales if you use pressure coupling).
> There's no such thing as a free lunch :-)
> Cheers,
> Erik

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