AMBER Archive (2007)

Subject: Re: AMBER: Prblm rgrdng Simulated Annealing

From: Anju Sharma (anju.020384_at_gmail.com)
Date: Wed Apr 11 2007 - 06:33:03 CDT

test cases?
u mean the tests tht are to be runned aftr compilation.... thn yes.

On 4/11/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
>
> did all of the test cases pass?
>
> On 4/11/07, Anju Sharma <anju.020384_at_gmail.com> wrote:
> > Hi,
> >
> > Wht i hv done so far is prepared dna str usng nucgen nd its .prmtop nd
> > inpcrd files r ready in vacuum as well as in water.
> > Now i wnt to run Simulated annealing so prepared following input file:
> >
> ---------------------------------------------------------------------------------
> > simulated annealing protocol, 20 ps
> >
> >
> > &cntrl
> >
> > nstlim=20000, pencut=-0.001, nmropt=1,
> > ntpr=200, ntt=1, ntwx=200,
> > cut=15.0, ntb=0, vlimit=10,
> > /
> >
> > &ewald
> > eedmeth=5,
> > /
> > &wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
> > value2=600., /
> > &wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
> > value2=100.0, /
> > &wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
> > value2=0.0, /
> >
> >
> > &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
> > value2=0.4, /
> > &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
> > value2=4.0, /
> > &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
> > value2=1.0, /
> > &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
> > value2=0.05, /
> >
> >
> >
> >
> > &wt type='END' /
> > ------------------------------------------------------------------
> >
> > Now whn i run dis file wth command
> >
> > sander -O -i anneal.in -o tga_ann.out -c tga_vac.inpcrd -p
> tga_vac.prmtop
> > -r tga_vac_ann.rst -x tga_vac_ann.traj
> >
> > thn dere is no error, immediately command prompt appears, bt dese
> output
> > files are nt generated
> >
> > Cn u pls tell me where m wrong, is dere is ny error in ny input file.
> > --
> > Anju Sharma
> > Project Fellow,
> > NIT, Hamirpur (H.P.)
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-- 
Anju Sharma
Project Fellow,
NIT, Hamirpur (H.P.)

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