Re: amber-developers: fix 1-4 scaling factor

From: Carlos Simmerling <>
Date: Thu, 21 Apr 2005 11:13:03 -0700

Dr. Yong Duan wrote:

>What I meant is in the input file. One can change the scaling
>factors during restart which, logically, is the continuation of a run.
>the notion "change during a run" is literaly untrue but logically
>correct :).
Users can also do many incorrect things in the input file, we see that
all the time. Putting things out of their reach isn't always consistent
with code
designed for researchers (not experimentalists that are playing with

what happened, did someone in your lab change the value during a
restart? ;-)

a more scary possibility is that I talked to someone recently using NAMD
run MD, and he used an amber prmtop but NAMD defaults to 1-4 scaling
of 1.0. So, people using NAMD with AMBER prmtops probably are getting
incorrect data (and publishing it as the "amber" force field). that's an
in favor of embedding it in the prmtop. another would be if glycam is
still going
to use mixed 1-4 scaling for glycoproteins.

Received on Wed Apr 05 2006 - 23:49:57 PDT
Custom Search