From: surendra negi (negi009_at_yahoo.com)
Date: Thu Feb 16 2006 - 11:22:03 CST
Hi Shen,
Yeah, I agree with you. Both of them are somehow
similar. You can generate consKFile and consKCol by
using
atomselect top "protein and name CA"
Hope this will work for you. Basically later is used
to prevent large fluctuation in the system. For detail
please refer NAMD manual.
thanks
surendra
--- Longzhu Shen <lzshen_at_emails.bjut.edu.cn> wrote:
> Am Mittwoch, 15. Februar 2006 16:50 schrieben Sie:
>
> Hello Negi,
>
> I read your reply to the Problem heating the system.
> I have some questions on
> it. Could you give me some explanations? Many
> thanks.
>
> In your script:
> ===============================
> # Fixed atoms for initial heating-up steps
> #
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile fix_backbone.pdb
> fixedAtomsCol B
>
> #
> # Restrained atoms for initial heating-up steps
> #
> constraints on
> consRef restrain_ca.pdb
> consKFile restrain_ca.pdb
> consKCol B
> ================================
> It seems that you use two ways of constraints
> simultaneously. Wondering why?
> In my opinion, the two only differ in the way to
> make constrains: one is
> applying for to the fixed atoms while the other use
> harmonic potential. So I
> suppose either will work for the system.
> Inaddition, can you tell me how to make consRef and
> consKFile files? Just
> the changing the value of one column , say beta, for
> the restrained atoms?
>
> Thanks for answering the question.
>
> sincerely,
>
> Longzhu Shen
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:38 CST