Hi Brad,
What exactly is unexpected about that? The zero of time is, I believe,
reset whenever irest = 0 (the default). The number of steps, on the other
hand, gets read from the restart file, I think no matter what. If you just
want to see that the trajectories are different, checking the potential and
kinetic energies should be both necessary and sufficient.
Also, you have temperature coupling turned off in your input (ntt=0) so the
nmropt changes to tautp probably aren't doing anything. That would require
ntt=1.
Regards,
Brian
On Wed, Oct 17, 2012 at 1:08 PM, Jordan, Brad <jbjordan.amgen.com> wrote:
> Hi,
>
> I'm performing an NMR refinement and would like to use a minimized
> structure and perform multiple refinements with ligand-protein NOEs. I'm
> trying to use the same protein structure each time, and just use a
> different random number seed to get an ensemble of results. I'm using AMBER
> 7, and I've set ig=different random numbers, but the calculation starts
> every time from the input coordinates at time 0.0 ps. Can someone help me
> figure out how to change this?
>
> Below is my input file:
>
> Thanks in advance!
>
> # 20 ps Simulated Annealing protocol
>
>
>
> &cntrl
> nstlim=20000, ntt=0,
> scee=1.2, ntx=1
> ntpr=500, pencut=1.0,
> ipnlty=1, nmropt=1,
> vlimit=10, ibelly=1
> ntb=0, ig=209858, tempi=10.
> igb=0,
> &end
>
> #
> #Simulated annealing protocol
> # from steps 0 to 5000 : raise target temperature 10-400K
> # from steps 5000 to 10000: leave at 400K
> # from steps 10000 to 40000 : re-cool to low temperatures
> #
> &wt type='TEMP0', istep1=0,istep2=5000,value1=600.,value2=600., &end
> &wt type='TEMP0', istep1=5001,istep2=18000,value1=600.,value2=100., &end
> &wt type='TEMP0', istep1=18001,istep2=20000,value1=0.0,value2=0.0, &end
>
> #
> #Strength of temperature coupling
> #
> &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,value2=0.4, &end
> &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,value2=4.0, &end
> &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,value2=1.0, &end
> &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,value2=0.05, &end
>
> #Restraint control - ramp up restraints over the first 3000 steps
>
> &wt type='REST', istep1=0,istep2=3000,value1=0.1,value2=1.0, &end
> &wt type='REST', istep1=3001,istep2=20000,value1=1.0,value2=1.0, &end
>
> &wt type='END', &end
> LISTOUT=POUT
> DISANG=RST
> Group Input for Ligand
> 1.0
> SEARCH
> RES 126
> END
> Group Input for Protein N-terminus:
> 1.0
> SEARCH
> RES 1 10
> FIND
> * * S *
> * * B *
> * * 3 *
> * * E *
> SEARCH
> RES 14
> RES 96
> RES 93
> RES 50
> RES 104
> RES 54
> RES 57
> RES 100
> RES 103
> RES 86
> RES 34
> RES 55
> END
> END
>
>
> Thanks,
>
> Brad
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Wed Oct 17 2012 - 11:00:03 PDT
