[gmx-users] Handling a very large system

[Ken Rotondi]

Thanks David,

Excuse me, I did mean...

constraints = all-angles

I had read about the issues with LINCS. Is it possible to apply the 
constraints to a sub-set of the system?

Sincerely,

Ken


On Jul 21, 2005, at 4:06 PM, David wrote:

> On Thu, 2005-07-21 at 15:55 -0400, Ken Rotondi wrote:

>> 2) I can constrain all angles in the system using:
>>
>>   constraints = all bonds

> this would constrain bonds only, which is fine. constraining angles
> gives problems with the LINCS algorithm although it may work with 
> SHAKE.
>
>>
>> in my .mdp file. Is it possible to apply these restraints to a sub-set
>> of all residues in the system?
>>
K.S. Rotondi Ph.D.
Research Fellow
The Gierasch Laboratory
Department of Biochemistry and Molecular Biology
University of Massachusetts-Amherst
Phone: 413-545-1250
Fax;      413-545-3291