AMBER Archive (2007)

Subject: AMBER: rst overflow for implicit REMD

From: In Hee Park (ipark_at_chemistry.ohio-state.edu)
Date: Tue Jun 26 2007 - 09:37:45 CDT

Dear Amber Users,

I was done successful GB-REMD run (1. increase Temp to the scaled target
Temp to obtain rst files for all replicas, 2. then real Temp exchange
among replicas) for my monomer system (120-residue) with Amber9 and then
extracted snapshots that I just needed for.

In the same manner, I wanted to apply the same GB-REMD procedure to my
dimer system (thus, 240-residue). However, I cannot go on to the real
Temp exchange step of REMD due to overflows of my rst files, in which
contain "*****" character instead of numerical values.

Although setting "iwrap=1" is recommended to keep the coordinate output
from overflowing the trajectory file format, this option can be used PME
run only. Now, it just shifting to explicit(or hybrid)-REMD the only
possible way to make my dimer REMD possible? Is there no way to resolve
the overflow problem under GB?

Thanks for your helps in advance...

_____________
In-Hee Park
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