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 :
*************************************************************************
***************************** md.in *****************************
*************************************************************************
100 ps MD production at constant T= 300K & P= 1Atm and coupling = 5..0
&cntrl
imin=0, ntx=7, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
nscm=5000,
ntf=2, ntc=2,
ntb=2, ntp=1, tautp=5.0, taup=5.0,
nstlim=50000, t=0.0, dt=0.002,
cut=9.0,
ntt=1,
irest=1
&end
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
--
__________________________________________________________________
Fabien Cailliez Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique e-mail : cailliez.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________
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Received on Mon Jun 28 2004 - 15:53:01 PDT
