Hi! I've contacted my partner and he told me they were overwritting the
files, so sadly I don't have the file with the problem.
He explained to me that when he tried to run the calculation in Parallel
mode it showed this problem (as it shows in the Image I've first attached
to the beginning of this thread) but like a workaround he tried to run it
with "sander" in parts... and doing that the problem was "fixed" in some
way but I took way too much time compared to using parallel mode.
Can you think what could be the problem while trying it with Parallel mode
because so it fails... but when running it with Sander it works?
Thanks!
On Tue, Jul 17, 2018 at 7:31 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> Thanks. Warming quickly at the beginning might be a problem, even with
> restraints. At what mdin and step do you see the first NaN, for example?
>
> <div>-------- Original message --------</div><div>From: Jorge Curima <
> curimax.07.gmail.com> </div><div>Date:07/17/2018 2:25 PM (GMT-08:00)
> </div><div>To: amber.ambermd.org </div><div>Subject: Re: [AMBER] Problem
> with NaN and Asteriks </div><div>
> </div>Ok! I write with '***' the filenames...
>
> *** min1.in
>
> minimización inicial de M y H2O (50%)
> &cntrl
> imin = 1,
> maxcyc = 5000,
> ncyc = 1000,
> ntb = 1,
> ntr = 1,
> cut = 10
> /
> manteniendo solutos fijos
> 500.0
> RES 1 247
> END
> END
>
> *** min2.in
>
> minimización inicial de la rafinosa y h2o con Cl (50%)
> &cntrl
> imin = 1,
> maxcyc = 50000,
> ncyc = 10000,
> ntb = 1,
> ntr = 0,
> cut = 10.0
> /
>
> END
>
> *** heat.in
>
> 20ps MD with res on M5Cl
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> nstlim=250000,
> dt=0.002,
> ntf=2,
> ntc=2,
> tempi=0.0,
> temp0=0.0,
> ntpr=100,
> ntwr=1000,
> ntwx=100,
> cut=10.0,
> ntb=1,
> ntp=0,
> ntt=3,
> gamma_ln=1.0,
> nmropt=1,
> ig=-1,
> /
> Keep mel fixed with weak restraints
> 500.0
> RES 1 247
> END
> /
> &wt type='TEMP0', istep1=0, istep2=2500, value1=0.0, value2=450.0 /
> &wt type='TEMP0', istep1=2501, istep2=25000, value1=450.0, value2=450.0 /
> &wt type='TEMP0', istep1=25001, istep2=35000, value1=450.0, value2=430.0 /
> &wt type='TEMP0', istep1=35001, istep2=40000, value1=435.0, value2=420.0 /
> &wt type='TEMP0', istep1=40001, istep2=60000, value1=420.0, value2=405.0 /
> &wt type='TEMP0', istep1=60001, istep2=80000, value1=405.0, value2=390.0 /
> &wt type='TEMP0', istep1=80001, istep2=100000, value1=390.0, value2=375.0 /
> &wt type='TEMP0', istep1=100001, istep2=120000, value1=375.0, value2=360.0
> /
> &wt type='TEMP0', istep1=120001, istep2=140000, value1=360.0, value2=345.0
> /
> &wt type='TEMP0', istep1=140001, istep2=160000, value1=345.0, value2=330.0
> /
> &wt type='TEMP0', istep1=160001, istep2=180000, value1=330.0, value2=315.0
> /
> &wt type='TEMP0', istep1=180001, istep2=200000, value1=315.0, value2=300.0
> /
> &wt type='TEMP0', istep1=200001, istep2=220000, value1=300.0, value2=300.0
> /
> &wt type='TEMP0', istep1=220001, istep2=240000, value1=300.0, value2=300.0
> /
> &wt type='TEMP0', istep1=240001, istep2=250000, value1=300.0, value2=300.0
> /
> &wt type='END'
> /
> END
>
> *** cpptraj.in
>
> parm M_wat50.prmtop
> trajin M_wat50_NVT188-189image.mdcrd
> hbond All out All.hbvtime14.dat solventdonor :WAT solventacceptor :WAT.O
> donormask :mel.N4,N5,N6 acceptormask :mel.N1,N2,N3 avgout All.UU.avg14.dat
> solvout All.UV.avg14.dat se$
> run
> write All14.dat All[UU] All[UV]
> runanalysis lifetime out time_HB14.dat All[solutehb] All[solventhb]
>
> *** HB.in
>
> #-- considerando los primeros 250 ps NVT con Tip3p y analizados cada 1 ps
>
> trajin polipro_cat_wat_nvt40.mdcrd
> image origin center familiar
>
> #-- Donors from pro
>
> donor mask :PRO.O
>
> #-- Acceptors from cat
>
> acceptor mask :cat.O5 :cat.H13
>
> #-- series hbt is just a placeholder to ensure we get the full analysis. If
> you don't
> #have the word series you don't get a full analysis.
> hbond print .01 series hbt
>
> *** NPT.in
>
> Melamine 50% in water: 500 ps MD equilibración
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, ig = -1, gamma_ln = 1.0,
> nstlim = 250000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 5000
> /
>
> *** NVT.in
>
> Sacarosa al 50%, gluco y lisina con agua: 500 ps MD equilibración
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 1, ntp = 0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 1, tautp = 10.0,
> nstlim = 250000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 5000
> /
>
> END
>
> *** reimage.in
>
> trajin M_wat50_NVT188.mdcrd
> trajin M_wat50_NVT189.mdcrd
> trajout M_wat50_NVT188-189image.mdcrd
> image familiar
> go
>
>
>
> On Tue, Jul 17, 2018 at 5:58 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > Better to paste them in, they shouldn't be big.
> >
> > Bill
> >
> > <div>-------- Original message --------</div><div>From: Jorge Curima <
> > curimax.07.gmail.com> </div><div>Date:07/17/2018 1:44 PM (GMT-08:00)
> > </div><div>To: amber.ambermd.org </div><div>Subject: Re: [AMBER] Problem
> > with NaN and Asteriks </div><div>
> > </div>Thanks for answering Bill.
> >
> > Here I attach a compressed file with all the ".in" files
> >
> > On Tue, Jul 17, 2018 at 4:24 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> > > To debug, first see where the values go off he rails.
> > >
> > > What equilibration was used? E.g. post min.in, md.in files.
> > >
> > > Bill
> > >
> > >
> > > On 7/17/18 11:59 AM, Jorge Curima wrote:
> > > > Hello, I'm a student at the Universidad Tecnologica Nacional -
> Facultad
> > > > Regional Resistencia in Resistencia, Argentina.
> > > >
> > > > I'm helping a Chemistry Research Group at my University.
> > > >
> > > > We are working with Amber 14 on a Debian 8.5 Server System.
> > > >
> > > > We are having trouble with certain calculation. I attach an Image of
> > the
> > > > Issue.
> > > >
> > > > I don't know if there is a certain format to post a question or
> issue,
> > > so I
> > > > apologize in advance, and hope if there is some, I would be grateful
> if
> > > > someone could notice me about it.
> > > >
> > > > Thanks in advance.
> > > >
> > > >
> > > > _______________________________________________
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Received on Sat Jul 21 2018 - 07:00:04 PDT
