Hello,
I had a problem doing some basic reweighting with REMD on AMBER11 when I
wanted to check the consistency
between mdcrds and mdouts. I noticed there is a discrepancy between the two.
Here is the information for
the temperature time series according to the 1)mdout, 2)mdcrd and 3) rem.log
note: ntwx=ntpr=500=10*nstlim
According to this, the rem.log and mdcrds are consistent, but the mdout does
not follow the same "replica series"
I wonder what is the source of this inconsistency or if perhaps I am missing
something. I apologize if this
has been previously addressed.
$ grep TEMP0 mdout.1 | head
TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# =
10
TEMP0 = 257.0000 REPNUM = 1 EXCHANGE# =
20
TEMP0 = 375.5300 REPNUM = 1 EXCHANGE# =
30
TEMP0 = 375.5300 REPNUM = 1 EXCHANGE# =
40
TEMP0 = 457.0000 REPNUM = 1 EXCHANGE# =
50
TEMP0 = 375.5300 REPNUM = 1 EXCHANGE# =
60
TEMP0 = 457.0000 REPNUM = 1 EXCHANGE# =
70
TEMP0 = 300.0000 REPNUM = 1 EXCHANGE# =
80
TEMP0 = 457.0000 REPNUM = 1 EXCHANGE# =
90
TEMP0 = 257.0000 REPNUM = 1 EXCHANGE# =
100
$ grep REMD remd.mdcrd.000 | head
REMD 1 10 500 300.000
REMD 1 20 1000 257.000
REMD 1 30 1500 375.530
REMD 1 40 2000 457.000
REMD 1 50 2500 375.530
REMD 1 60 3000 457.000
REMD 1 70 3500 457.000
REMD 1 80 4000 257.000
REMD 1 90 4500 457.000
REMD 1 100 5000 300.000
$ awk '$1==1 {print $5}' rem.log | awk 'NR%10==0{print}' | head
300.00
257.00
375.53
457.00
375.53
457.00
457.00
257.00
457.00
300.00
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Fri Feb 11 2011 - 02:30:04 PST
