AMBER Archive (2007)

Subject: Re: AMBER: Prblm rgrdng Simulated Annealing

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Apr 11 2007 - 06:23:43 CDT

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.)
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu