[AMBER] problem rejoining segmented out files in long simulation

From: g t <sketchfoot.googlemail.com>
Date: Wed, 28 Apr 2010 16:04:59 +0100

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:


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 =
 Etot = -65097.5659 EKtot = 15993.4386 EPtot =
 BOND = 480.0218 ANGLE = 1275.2825 DIHED =
 1-4 NB = 565.9616 1-4 EEL = 7122.1569 VDWAALS =
 EELEC = -102028.9421 EHBOND = 0.0000 RESTRAINT =
 DV/DL = -0.2145
 EKCMT = 7087.7220 VIRIAL = 7056.5130 VOLUME =
                                                    Density =
 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

Kind regards,
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Received on Wed Apr 28 2010 - 08:30:03 PDT
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