AMBER Archive (2002)

Subject: Re: ramdomized start velocities

From: James W. Caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Fri Nov 08 2002 - 14:35:39 CST

Nope, the default input to sander acually contains
the random number seed. To get different trajectories
you need to input different seeds. See variable "IG"
in the sander input section 5.6.10.

jim

On Fri, 8 Nov 2002, Arvid Soederhaell wrote:

>Dear ambers
>
>This is probably something that I should know...
>
>I have a 6 aminoacids long peptide which i want to run a simulated
>annealing on, that is simply generate lots of random conformations. I have
>a script that i use to generate a series of inputfiles and then I run
>these identical inputfiles. What then happens is that all structures that
>are generated are identical! I thought that the start velocities in an MD
>run are supposed to be random, and hence follow different trajectories...
>What have i done wrong?
>
>Here is the input:
>
> &cntrl
> imin=0, nmropt=1,
> ibelly=0, ntr=0,
> ntx=1, ntpr=1000, ntwx=0, ntwv=0, ntwe=0,
>
> ntf=2, ntc=2,
> ntb=1, ntp=0,
> dielc=1, cut=8.0, nsnb=10.0,
> scnb=2.0, scee=1.2,
>
> nstlim=25000, dt=0.001,
> temp0=300, tempi=300, ntt=4, tautp=0.2,
> &end
> &wt type='TEMP0',
> istep1=1, istep2=1000,
> value1=300, value2=300,
> &end
> &wt type='TEMP0',
> istep1=1001, istep2=5000,
> value1=300, value2=1500,
> &end
> &wt type='TEMP0',
> istep1=5001, istep2=20000,
> value1=1500, value2=1500,
> &end
> &wt type='TEMP0',
> istep1=20001, istep2=23000,
> value1=1500, value2=0,
> &end
> &wt type='END',
> &end
>
>
>
>
>Arvid Soderhall
> 

-- 

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James W. Caldwell                         (voice) 415-476-8603
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