"In most cases I believe this will be the first entry of a set
of multipl dihedrals. (Either the first or the last, not sure which) But all
multiple dihedrals should have the same entry for SCEE and SCNB anyway in
the original frcmod/parmXX.dat file in the first place."
Speaking of... When I first started putting the info into our parm file, I tried adding it just to the first comment in a multi-term dihedral. But, that didn't work. So, I added it to them all, and it worked. It hadn't occurred to me to use just the last entry. This needs to be documented... Is it the last entry?
Also, it has come to our attention that there are occasional, subtle discrepancies between file specs and actual implementation. We've been haphazardly compiling a list. At some point in the future, I intend to offer to make the docs and the files match each other.
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: Ross Walker [ross.rosswalker.co.uk]
Sent: Wednesday, April 06, 2011 1:25 PM
To: 'AMBER Developers Mailing List'
Subject: Re: [AMBER-Developers] variable 1-4 scaling
> If you can simply emulate this behavior, that would be great. Only
> sleap
> can write these files, but they're indexed in exactly the same way as
> the
> dihedral force constants, etc. I don't recall how multi-term dihedrals
> were
> treated, but I think only the first scaling factor was used (since they
> should all be identical). You don't want to scale it multiple times,
> though.
Things should NOT be scaled multiple times. The 'one' that gets used is the
one corresponding to the dihedral that is actually used in doing the 1-4
calculation. In most cases I believe this will be the first entry of a set
of multipl dihedrals. (Either the first or the last, not sure which) But all
multiple dihedrals should have the same entry for SCEE and SCNB anyway in
the original frcmod/parmXX.dat file in the first place. If they don't then
the user is in a whole world of pain from the beginning.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
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Received on Wed Apr 06 2011 - 11:00:03 PDT
