Re: [gmx-users] Analyse REMD
tit=0
>}
> }
> if(printnextround){
>printit=1
> }
>}
> }' > $2
> }
>
>
> # Step 0: cleanup
> rm -f _ERROR_ problems* z* fixed.log*
>
>
> # Step 1: Find any problems
> # this tr command is necessary in case there was corruption in the .log file
> cat $LOG | tr -d '\0' > my.log
> find_problems my.log
>
> # Step 2: Fix any problems
> n=0
> cp problems problems.$n
> cp problems.init problems.init.$n
> cp z z.$n
>
> cat problems.0 | while read line; do
> # exit the loop if there are no more problems
> if (($(cat problems|wc -l)==0)); then
>break
> fi
> let "n++"
> fn=($line)
> fix_problems my.log fixed.log ${fn[0]} ${fn[1]} $STEP
> cp fixed.log fixed.log.${n}
> cp fixed.log my.log
> find_problems fixed.log
> cp problems problems.$n
> cp problems.init problems.init.$n
> cp z z.$n
> done
>
>
> # Want this file fixed.log to always exist so that I can use it in the DEMUX
> scripts
> if [ ! -e fixed.log ]; then
> mv my.log fixed.log
> else
> rm my.log
> fi
> # Find any problems
> find_problems fixed.log
>
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of YanhuaOuyang
> <15901283...@163.com>
> Sent: 22 May 2016 04:48:53
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Analyse REMD
>
> Hi, I have run a REMD, which including 46 replicas. I searched how to analyze
> my REMD statistics, but I am still confused how to analyze my result; how to
> generate a continuous a energy distribution curve; how to deal with 46 .log
> files. It seems so complicated.
>
> one of my md.log file is as below:
> Replica exchange at step 998000 time 1996.0
> Repl 18 <-> 19 dE_term = 1.690e+01 (kT)
> Repl ex 01234 x 56 x 78 x 9 10 11 12 13
> 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
> 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
> 45
> Repl pr .01 .17 .03 1.0 1.0 .00 .00
> .01 .00 .00 .00 .00 .00 .00 .00
> .00 .00 .00 .00 .00 .00 .00 .00
>
> Replica exchange statistics
> Repl 499 attempts, 250 odd, 249 even
> Repl average probabilities:
> Repl 0123456789 10 11 12 13
> 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
> 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
> 45
> Repl .07 .08 .05 .05 .06 .06 .06 .06 .06 .05 .05 .04 .03
> .05 .03 .03 .03 .01 .03 .02 .04 .02 .02 .02 .01 .02 .02 .01
> .01 .01 .01 .01 .01 .01 .01 .02 .01 .01 .02 .00 .02 .00 .02
> .02 .01
> Repl number of exchanges:
> Repl 0123456789 10 11 12 13
> 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
> 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
> 45
> Repl 14 20 13 12 16 14 15 17 14 159 128
> 13757256 1064625316
>333234523424244
> 3
> Repl average number of exchanges:
> Repl 0123456789 10 11 12 13
> 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
> 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44
> 45
> Repl .06 .08 .05 .05 .06 .06 .06 .07 .06 .06 .04 .05 .03
> .05 .03 .02 .03 .01 .02 .02 .04 .02 .02 .02 .01 .02 .01 .00
> .02 .01 .01 .01 .01 .01 .02 .02 .01 .01 .02 .01 .02 .01 .02
> .02 .01
> I wonder whether the result is ideal, do I need to optimize my temperature
> distribution.
>
> Best regards
> ouyang
> --
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Re: [gmx-users] Analyse REMD
1]} $STEP
cp fixed.log fixed.log.${n}
cp fixed.log my.log
find_problems fixed.log
cp problems problems.$n
cp problems.init problems.init.$n
cp z z.$n
done
# Want this file fixed.log to always exist so that I can use it in the DEMUX
scripts
if [ ! -e fixed.log ]; then
mv my.log fixed.log
else
rm my.log
fi
# Find any problems
find_problems fixed.log
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of YanhuaOuyang
<15901283...@163.com>
Sent: 22 May 2016 04:48:53
To: gmx-us...@gromacs.org
Subject: [gmx-users] Analyse REMD
Hi, I have run a REMD, which including 46 replicas. I searched how to analyze
my REMD statistics, but I am still confused how to analyze my result; how to
generate a continuous a energy distribution curve; how to deal with 46 .log
files. It seems so complicated.
one of my md.log file is as below:
Replica exchange at step 998000 time 1996.0
Repl 18 <-> 19 dE_term = 1.690e+01 (kT)
Repl ex 01234 x 56 x 78 x 9 10 11 12 13
14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
Repl pr .01 .17 .03 1.0 1.0 .00 .00
.01 .00 .00 .00 .00 .00 .00 .00
.00 .00 .00 .00 .00 .00 .00 .00
Replica exchange statistics
Repl 499 attempts, 250 odd, 249 even
Repl average probabilities:
Repl 0123456789 10 11 12 13
14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
Repl .07 .08 .05 .05 .06 .06 .06 .06 .06 .05 .05 .04 .03 .05
.03 .03 .03 .01 .03 .02 .04 .02 .02 .02 .01 .02 .02 .01 .01 .01
.01 .01 .01 .01 .01 .02 .01 .01 .02 .00 .02 .00 .02 .02 .01
Repl number of exchanges:
Repl 0123456789 10 11 12 13
14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
Repl 14 20 13 12 16 14 15 17 14 159 128 13
757256 10646253163
332345234242443
Repl average number of exchanges:
Repl 0123456789 10 11 12 13
14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
Repl .06 .08 .05 .05 .06 .06 .06 .07 .06 .06 .04 .05 .03 .05
.03 .02 .03 .01 .02 .02 .04 .02 .02 .02 .01 .02 .01 .00 .02 .01
.01 .01 .01 .01 .02 .02 .01 .01 .02 .01 .02 .01 .02 .02 .01
I wonder whether the result is ideal, do I need to optimize my temperature
distribution.
Best regards
ouyang
--
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[gmx-users] Analyse REMD
Hi, I have run a REMD, which including 46 replicas. I searched how to analyze my REMD statistics, but I am still confused how to analyze my result; how to generate a continuous a energy distribution curve; how to deal with 46 .log files. It seems so complicated. one of my md.log file is as below: Replica exchange at step 998000 time 1996.0 Repl 18 <-> 19 dE_term = 1.690e+01 (kT) Repl ex 01234 x 56 x 78 x 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Repl pr .01 .17 .03 1.0 1.0 .00 .00 .01 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 .00 Replica exchange statistics Repl 499 attempts, 250 odd, 249 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Repl .07 .08 .05 .05 .06 .06 .06 .06 .06 .05 .05 .04 .03 .05 .03 .03 .03 .01 .03 .02 .04 .02 .02 .02 .01 .02 .02 .01 .01 .01 .01 .01 .01 .01 .01 .02 .01 .01 .02 .00 .02 .00 .02 .02 .01 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Repl 14 20 13 12 16 14 15 17 14 159 128 13 757256 10646253163 332345234242443 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Repl .06 .08 .05 .05 .06 .06 .06 .07 .06 .06 .04 .05 .03 .05 .03 .02 .03 .01 .02 .02 .04 .02 .02 .02 .01 .02 .01 .00 .02 .01 .01 .01 .01 .01 .02 .02 .01 .01 .02 .01 .02 .01 .02 .02 .01 I wonder whether the result is ideal, do I need to optimize my temperature distribution. Best regards ouyang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
