where are you setting pk to zero, in the prmtop or parm.dat or frcmod?
Also is it possible that other dihedral terms are being applied to this
rotation,
and if you set pn to 0 or 1 you are replacing different terms? meaning
the energy difference is not from the pk=0 term, but from a change in
which other terms are present?
richard dimelow wrote:
> 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.ilion.bio.sunysb.edu>
> To: <amber.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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Received on Tue Feb 07 2006 - 06:10:05 PST
