I don't know the answer, but if it's the dv/dl data you're after, it might
help to put this in the subject line and say it earlier in your email.
Whoever might be able to help would be very likely to miss this point.
On Wed, Apr 28, 2010 at 11:04 AM, g t <sketchfoot.googlemail.com> wrote:
> Hello all,
>
> I was hoping someone could help me with analyzing the setup in my
> ti_calculations. I am limited by my cluster to running jobs of 48 hours
> only. Therefore, I am using a script that splits a large job of nanoseconds
> into multiple segments of around 40 picoseconds. The script waits for a
> unique restart file to be written and submits the next segment. As a
> result,
> I get multiple .out and .crd files:
>
> e.g.
>
> hexanol_complex_prod_v0_l7_no1.out (50-90 picoseconds)
> NSTEP = 20000
> hexanol_complex_prod_v0_l7_no2.out (90-130 picoseconds)
> NSTEP = 20000
> hexanol_complex_prod_v0_l7_no3.out (130-170 picoseconds)
> NSTEP = 20000
> hexanol_complex_prod_v0_l7_no4.out (170-210 picoseconds)
> NSTEP = 20000
> hexanol_complex_prod_v0_l7_no5.out (210-250 picoseconds)
> NSTEP = 20000
>
> Rejoining the .crd files with ptraj is not a problem. However getting the
> data from the out file has been troublesome. The problem is that upon
> restarting, all the recorded numbers in the outfile are averaged for the
> number of steps of that segment only. i.e. I don't get an average that
> includes all the steps that preceded it
>
> e.g. for hexanol_complex_prod_v0_l7_no2.out:
>
>
>
> A V E R A G E S O V E R 20000 S T E P S
>
>
> NSTEP = 20000 TIME(PS) = 130.000 TEMP(K) = 299.91 PRESS =
> 5.5
> Etot = -65097.5659 EKtot = 15993.4386 EPtot =
> -81091.0045
> BOND = 480.0218 ANGLE = 1275.2825 DIHED =
> 1629.2670
> 1-4 NB = 565.9616 1-4 EEL = 7122.1569 VDWAALS =
> 9865.2479
> EELEC = -102028.9421 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> DV/DL = -0.2145
> EKCMT = 7087.7220 VIRIAL = 7056.5130 VOLUME =
> 261867.6828
> Density =
> 1.0197
> Ewald error estimate: 0.7137E-04
>
>
> These numbers don't take into account the preceding 50 picoseconds. Only
> the
> time seems to have continued on from the previous segment.
>
> I have set ntpr to write every 1000 steps and have wriitten a script to
> average the dv/dl values that i am interested in. However in a test
> situation the averages calculated with the script do not match that in the
> 'A V E R A G E S O V E R 20000 S T E P S' section. Would it be accurate
> to just average all the dv/dl values in the 'A V E R A G E S O V E R
> 20000 S T E P S' section? It is impossible to check manually because of the
> random seed issue.
>
> Any advice on recalculation of segmented outfiles would be greatly
> apprecaited.
>
> Kind regards,
> GT
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Received on Wed Apr 28 2010 - 08:30:04 PDT
