AMBER Archive (2004)

Subject: AMBER: jump in temperature + problem in trajectory files

From: cailliez (
Date: Mon Jun 28 2004 - 09:11:14 CDT

Dear Amber users,

I am running MDs with AMBER7 (with all the patches for debug included in
the code) and I saw two
strange things.
1) I am running these MDs on a big cluster of SGI ORIGIN 3800 on 16
processors (my system
is quite big, almost 100000 atoms). During the 7.5 ns I already have, my
protein seems to behave "normally", except during approximately 100 ps
(after around 7 ns) during which the temperature jumped from 300K to
305K (and as a consequence there are also density jumps, volume jumps,
energy jumps at the same time). And then the temperature goes down to
300K. This jump is quite big and I wonder if anyone would have any idea
to explain this.
My input file is :
***************************** *****************************
100 ps MD production at constant T= 300K & P= 1Atm and coupling = 5.0
    imin=0, ntx=7, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
    ntf=2, ntc=2,
    ntb=2, ntp=1, tautp=5.0, taup=5.0,
    nstlim=50000, t=0.0, dt=0.002,

2) My second question is about trajectory files. During my dynamics
three of my trajectory files have been "corrupted" and I cannot use them
to analyze this moment of the trajectory. When I restart my MD for the
same period of time, I now have good trajectory files (the files .out,
.rst, .ene are OK). Does anyone ever had this problem or can explain it ?

Thanks for your answers,

Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail :
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					

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