AMBER Archive (2002)

Subject: Minimization in GB-SA-E-Spikes, LINMIN

From: Sarangan Ravichandran (sravi_at_ncifcrf.gov)
Date: Tue Jul 16 2002 - 10:02:58 CDT

HI All:

I am using GB model to do minimization
of a protein in SANDER (AMBER7). The script
to do minimization is as follows

------------------
&cntrl
 imin=1, maxcyc=5000
 cut=300.0, igb=2, saltcon=0.1, gbsa=1,
 ntpr = 20, ntx=1, ntb=0,
 ntwx=500,
 &end
--------------------
During minimization,
I keep seeing energy spikes at regular
intervals (ex 100 steps in some cases) after
few 1000 steps. My starting configuration has
no bumps and the energy is close to zero.
I also have the LINMIN FAILURE message during
minimization. I am aware of the web-page in amber
home which discusses LINMIN issues. My question is
how to handle the energy spikes and LINMIN failures.

Thanks

Ravi