Amber 11 pmemd.cuda fails to get a meaningful results with the following
input, but with the second one works fine. All available bugfixes including
11th were applied. The output files are attached to the mail. Surprisingly,
all steps were completed, but with NaN bond and huge angle energy values.
Also coordinates became infinite.
Stage 4 - density equilibration
&cntrl
imin=0,irest=1,ntx=5,
nstlim=25000,dt=0.002,
igb=0, ntc=2,ntf=2,ntp=1, taup=1,
cut=10.0, ntb=2,
ntpr=500, ntwx=500, ntwr=25000,
iwrap=1,
ioutfm=1, ig=75397747,
ntt=3, gamma_ln=2.0, temp0=300.0,
* ntr=1*,
&end
Restraints for PMEMD
2.0
RES 1 1
END
END
Stage 4 - density equilibration
&cntrl
imin=0,irest=1,ntx=5,
nstlim=25000,dt=0.002,
igb=0, ntc=2,ntf=2,ntp=1, taup=1,
cut=10.0, ntb=2,
ntpr=500, ntwx=500, ntwr=25000,
iwrap=1,
ioutfm=1, ig=75397747,
ntt=3, gamma_ln=2.0, temp0=300.0,
* ntr=0,*
&end
Restraints for PMEMD
2.0
RES 1 1
END
END
*
$ uname -a*
Linux 2.6.31.5-127.fc12.x86_64 #1 SMP Sat Nov 7 21:11:14 EST 2009 x86_64
x86_64 x86_64 GNU/Linux
*$ cudafe --version*
cudafe: NVIDIA (R) Cuda Language Front End
Portions Copyright (c) 2005-2010 NVIDIA Corporation
Portions Copyright (c) 1998-2005 Edison Design Group Inc.
Based on Edison Design Group C/C++ Front End, version 4.1 (Nov 3 2010
16:25:55)
Cuda compilation tools, release 3.2, V0.2.1221
--
Sincerely,
Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Sun Jan 02 2011 - 06:30:03 PST
