Re: contraint failure in RATTLE algorithm

From: ELENA JEAN LEVIN (ejlevin_at_wisc.edu)
Date: Thu Nov 06 2003 - 16:01:07 CST

Hi Brian,
 
Thanks for the suggestions. Upgrading to version
2.5 is unfortunately not an immediate option, as
our sys admin person is busy for the next few
days. We tried gradually increasing the
temperature, as you suggested, using the following
script:
 
reassignFreq 1000
reassignTemp 25
reassignIncr 25
reassignHold 300
 
numsteps 50000
minimize 1000
reinitvels 0
 
However, we got the same error message. We tried
running the entire simulation at 1 Kelvin and
still had the RATTLE error, so I don't think that
a sudden jump in temperature is the problem. Do
you have any other ideas?
 
Thanks,
Elena
  
----- Original Message -----
From: Brian Bennion <brian_at_youkai.llnl.gov>
Date: Thursday, November 6, 2003 2:10 pm
Subject: Re: namd-l: contraint failure in RATTLE
algorithm
  
> Hello Elena
>
> First suggestion, try the final 2.5 version of
NAMD, if nothing
> else it
> will clean up the log file.
>
> Second, and I hope Jim or somone else will
correct me if I am
> wrong, but
> the protein-rattle algorithm can't handle a
single energy pulse of
> 313K.
> I have received similar warnings when first
using namd without
> first
> trying to
> heat the protein/water system gradually.
>
> Brian
   
  

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:17:54 CST