AMBER Archive (2002)

Subject: Re: ramdomized start velocities

From: Andy Purkiss (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Fri Nov 08 2002 - 13:28:46 CST

You need to set the random number seed ig to different values to get a
range of conformations, any value should do.

This is because random numbers are not really random, but part of a
defined sequence which looks random.

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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