Hi Scott,
Here is the input file
Initial minimization w/ position restraints on DNA, 9.0 cut
&cntrl
nmropt = 0,
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 1000, ntwx = 10000, ntwv = 0, ntwe = 0,
ntwprt = 0, ntwr = 10000, iwrap = 1, ioutfm = 1,
ntf = 2, ntb = 2, dielc = 1.0,
cut = 9.0,
ipol = 0,
ibelly = 0, ntr = 0,
nstlim = 2000000,
nscm = 1000,
t = 0.0, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ig = 71277, heat = 0.0,
ntt = 1, dtemp = 0.0,
tautp = 1.0,
ntp = 1, pres0 = 1.0, comp = 44.6,
taup = 1.0, ntc = 2, tol = 0.0005,
&end
&ewald
&end
On Thu, Apr 18, 2013 at 6:26 AM, Scott Le Grand <varelse2005.gmail.com>wrote:
> Could you send me the inputs to the simulation?
> On Apr 17, 2013 11:05 AM, "HIMANSHU JOSHI" <himanshuphy87.gmail.com>
> wrote:
>
> > Dear friends,
> >
> > I am running pmemd.cuda.MPI for a system with approximately 1/2 million
> > atoms with dna and wate, After energy min and equilibration, I tried to
> do
> > production run with constant pressure (flag : ntb =2 ntp =1) but its
> > giving error *** in the restart file and energy values in output file
> after
> > running few steps (~ 30 ps). The same job with same input files is
> running
> > well in cpu version of pmemd (pmemd.mpi).
> >
> > Earlier the same system I ran with constant volume simulation (ntb = 1 )
> in
> > gpu with same pmemd.cuda.MPI and it ran well.
> >
> > So there is some problem with pmemd.cuda.MPI with npt simulation !!!
> >
> > Can anyone assure me.
> >
> > I have applied the latest bugfixes to amber 12 amber (Version 12.2) dated
> > (01/10/2013) for both cpu and gpu.
> >
> > Looking forward for some constructive comments from amber community .
> > Thanks for your kind attention.
> >
> >
> > --
> > *With Regards,
> > HIMANSHU JOSHI
> > Graduate Scholar, Center for Condense Matter Theory
> > Department of Physics IISc.,Bangalore India 560012*
> > ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
> > सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
> > <
> >
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--
*With Regards,
HIMANSHU JOSHI
Graduate Scholar, Center for Condense Matter Theory
Department of Physics IISc.,Bangalore India 560012*
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Received on Wed Apr 17 2013 - 23:00:02 PDT
