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.
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Tue Jul 17 2018 - 16:00:02 PDT
