[gmx-users] problem running posre

Alan Dodd anoddlad at yahoo.com
Tue Jan 30 15:27:55 CET 2007

Have you tried running for a short period without PR, then putting the output from that into PR again?  If the initial run is short enough, it shouldn't affect things too much, but may still randomise out whatever's causing the problem.

----- Original Message ----
From: andrea spitaleri <spitaleri.andrea at hsr.it>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, January 30, 2007 2:10:33 PM
Subject: [gmx-users] problem running posre

Hi all,
I am encountering in a very strange problem. Feeding a protein (after minimization) to a position 
restraints simulation after few steps (10-20) I am getting this crash error:
"Number of grid cells is zero. Probably the system and box collapsed"
However, submitting with the same input a simulation with "no" position restraints the runs goes 
fine. I tried using posrefc 1000 and lower (200). Same result.
Any suggestion?



Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
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