This happens around 500 ns or so. I checked the structure there is nothing
"crazy". Everything seems ok.
I am using the ff03.r1 force field, mbondi2 for PBradii as directed in the
manual.
On Fri, Oct 14, 2011 at 1:17 PM, E. Nihal Korkmaz
<enihalkorkmaz.gmail.com>wrote:
> 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
>
>
>
--
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 - 11:30:06 PDT
