AMBER Archive (2006)

Subject: Re: AMBER: increase force constants

From: Amber admin (amber-admin_at_scripps.edu)
Date: Thu Aug 24 2006 - 19:15:24 CDT

Carlos Simmerling writes:

have you looked at the section of the manual starting at page 178 (Amber9)?
this described the NMR refinement options. You'll want to set the RK values
differently from RKA values (ie. rk1 different from rk1a). You can list the
same restraint twice- once for the range you are changing and again for the
step range where it does not change. If the manual isn't clear, then let us
know which specific step you are having trouble with.

Mahalakshmi Sahasranaman wrote:

> Dear Amber Users,
>
> In restrained Molecular dynamics using NMR constraints, I would like
> to do a 20ps simulation. I want to increase linearly the force
> constants for all DNA-DNA constraints from 3.2 to 32 kcal over 3ps and
> remain at 32Kcal for final 17ps of the simulation. How to increase
> linearly the force constants for all DNA-DnA constraints from 3.2 to
> 32 kcal over 3ps and then remain at 32kcal for the final 17ps ? Please
> help me.
>
> Thanks,
> Lakshmi
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