Amber 11, I tried on GeForce GTX 480 and Tesla C2070 processors, on Linux
(CentOS release 5.6). We have Cuda 4 for nvidia compiler. I am running with
pmemd.cuda.
and that's my in file below (although same file works ok with the homologous
structure) :
&cntrl
imin=0,
ntb=0,
ntx=5,
irest=1,
ntpr=200,
ntwr=200,
ntwx=200,
ntwe=200,
nstlim=5000000,
dt=0.002,
ntt=3,
temp0=300,
tempi=300,
ig=-1,
tautp=1,
gamma_ln=20,
ntp=0,
pres0=1,
taup=1,
ntc=2,
tol=0.00001,
ntf=2,
ntb=0,
dielc=1,
cut=9999,
rgbmax=12,
ipol=0,
ifqnt=0,
igb=5,
saltcon=0.15,
ioutfm=1,
nscm=100,
&end
On Fri, Oct 14, 2011 at 1:05 PM, Scott Le Grand <varelse2005.gmail.com>wrote:
> What revision of AMBER? What GPU? What OS? What driver? What toolkit did
> you compile with?
>
>
>
> On Fri, Oct 14, 2011 at 10:55 AM, E. Nihal Korkmaz
> <enihalkorkmaz.gmail.com>wrote:
>
> > Dear all,
> >
> > I keep having a problem that only for a particular protein the
> simulation
> > "freezes" and by freeze I mean, it looks like the job is running but no
> > changes are made on the output files even if you wait 2 days. I am using
> > igb=5 on GPU, it is a 114 amino acid long protein, I have the homologous
> > structure running (112 amino acid long) without a problem. But that
> > specific
> > one stops without being dropped of the queue or any error messages at
> all.
> > I
> > checked the output files, no '*' or 'NaN' are present. I also tried
> running
> > on different machines, same thing happens. I tried starting from a
> > different
> > restart file, nothing changes. I always freezes although at different
> time
> > steps.
> >
> > Has anyone have such a problem before? What can be the causes? I'd
> > appreciate any comments or suggestions.
> >
> > Thanks,
> >
> > --
> > Elif Nihal Korkmaz
> >
> > Research Assistant
> > University of Wisconsin - Biophysics
> > Member of Qiang Cui & Thomas Record Labs
> > 1101 University Ave, Rm. 8359
> > Madison, WI 53706
> > Phone: 608-265-3644
> > Email: korkmaz.wisc.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Elif Nihal Korkmaz
Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644
Email: korkmaz.wisc.edu
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Received on Fri Oct 14 2011 - 11:30:03 PDT
