AMBER Archive (2006)

Subject: Re: AMBER: dihedral parameters

From: richard dimelow (r.dimelow_at_student.manchester.ac.uk)
Date: Mon Feb 06 2006 - 04:22:08 CST

i'm still a bit confused because i have set the force constant PK to zero
(with IDIVF=1), but i get a different energy depending on whether PN is 0 or
1. Looking at my mdout file it is the 1-4EEL energy term that is most
affected by this change.
cheers

----- Original Message -----
From: "Carlos Simmerling" <carlos_at_ilion.bio.sunysb.edu>
To: <amber_at_scripps.edu>
Sent: Saturday, February 04, 2006 5:30 PM
Subject: Re: AMBER: dihedral parameters

> if you look at the energy function, the angle is multiplied by
> the periodicity. A period of 0 means constant energy.
> To remove the 1-4 you need to remove the dihedrals altogether.
> there may be other ways if you want to manually modify the prmtop.
>
> richard dimelow wrote:
>> dear all
>> the dihedral parameters are listed in the .dat files as IDIVF PK
>> PHASE PN. Could some one tell me what happens if i set PN (the
>> periodicity value) to zero. Does this turn off the 1-4 interactions
>> between atoms 1 and 4 in the dihedral, for example?
>> cheers
>> rich
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