I can't seem to open those .ps files, acrobat distiller gives me a font
error.
can you convert them to jpegs or something easier for windows machines?
thanks
carlos
Peter Varnai wrote:
>Dear Amber users,
>
>I analyse a 50 ns long trajectory of a nucleic acid calculated by GB and
>Langevin dynamics (amber 8). I noticed that at regular intervals the rms
>and energy components had peaks:
>http://cus.cam.ac.uk/~pv232/amber/amber.html
>
>I used the following input:
> &cntrl
> ntx=5, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
> nstlim=500000, nscm=1000, ntf=2, ntc=2, ntb=0, ntp=0,
> irest=1, ntt=3, temp0=300, gamma_ln=5, cut=99.0, rgbmax=99, dt=0.002,
> ntr=0, saltcon=0.1, gbsa=1, surften=0.005, igb=1 &end
>
>I noticed that in the first 4 ns the peaks are more frequent which
>coincides with the fact that here I used nstlim=100000. That would mean
>that the restart of my trajectory fragments are not correct, but I am not
>sure why. Any suggestion what might have gone wrong would be appreciated.
>
>Thanks,
>Peter
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Received on Tue Apr 05 2005 - 17:53:00 PDT
