Thank you for your detailed steps! > 在 2016年5月31日，下午12:53，Christopher Neale <chris.ne...@alum.utoronto.ca> 写道： > > Dear Ouyang: > > There is a script in the gromacs package (at least up to 5.1.2) called > demux.pl . You can use it to get more human friendly information out of your > REMD runs ( see http://www.gromacs.org/Documentation/How-tos/REMD for some > very sparse info on demux.pl ). Basically you feed it the log file and it > provides you with some useful output files. You can then use the -demux > option to trjcat to get demuxed xtc files. The demux.pl script is not > perfect. The last time I looked it could not handle more than X frames (I > forget how many, but I and others posted fixes to the gmx mailing list a few > years ago). Also, it relies on a sensible .log file and if you (1) run REMD > then (2) have some type of crash or walltime overrun that does not give you > .cpt files then (3) you restart REMD and it runs fine past the point of the > previous crash, then demux.pl will give you good data. However, if you go > through steps 1 and 2 above and then you restart REMS and it crashed again > before you get to the > point of the first crash then even if you again restart and you pass this > point the log file will never be OK for demux.pl . I have some scrips that > can recover from such an error but they are generally not necessary unless > you have a run on a cluster that is unstable over some period. I have pasted > my fix script below for posterity, though you very likely don't need it. > > $ cat checkforproblems.sh > # This script finds and fixes any problems in the log file prior to demuxing > # When this script is done: > # if the ./problems file is empty then everything was fixed (or no problems > ex > isted) > # if the ./problems file is NOT empty, then some problem remain > # > # Command line input parameters: > # $1 = the number of MD integration steps between exchange attempts > # $2 = the location of the log file to use > > STEP=$1 > LOG=$2 > > function find_problems { > # $1 = log file > grep "^Replica exchange at step" $1 |awk '{if($5!=last+'$STEP')print > $5,last;l > ast=$5}' > problems.init > if (($(cat problems.init|wc -l)!=0)); then > cat problems.init | awk '{printf("%d\t",$2);if(NR%2==0)printf("\n")}' > > prob > lems > else > rm -f problems > touch problems > fi > grep "^Replica exchange at step" $1 |awk '{print $5,last;last=$5}' > z > } > > function fix_problems { > # $1 = log file input > # $2 = log file output > # $3 = low cut > # $4 = high cut > # $5 = step > cat $1 |awk ' > BEGIN{ > part=0; > step='$5' > foundlow=0 > foundhigh=0 > printjustonemore=0 > printnextround=0 > ##print "Fixing with:","'$1'","'$2'",'$3','$4','$5' >> > "./FIX_PROBLEMS_INPUT > " > } > > { > if(part==0){ > if($1=="Replica"&&$2=="exchange"&&$3=="at"&&$4="step"){ > part=1 > n=$5 > if(n=='$3'){ > foundlow++ > } > if(n=='$4'){ > foundhigh++ > } > if(foundlow==0){ > # output if we did not yet find the low cutoff > printit=1 > }else{ > # found the low cutoff > if(foundhigh==0){ > # want to print the low cutoff once, so use the printjustonemore > var > iable to do so, then reset printit variable after output > printjustonemore=1 > }else{ > # Now only ouput if we have seen the first occurrence of the high > cu > toff, but dont want this value, so use the printnextround variable > printnextround=1 > } > } > } > }else{ > if($1!="Repl"){ > part=0 > # Print a sinfle blank line after each replica segment > print "" > } > } > if(part){ > if(printit){ > print $0 > if(printjustonemore){ > printjustonemore=0 > printit=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 1996.00000 > Repl 18 <-> 19 dE_term = 1.690e+01 (kT) > Repl ex 0 1 2 3 4 x 5 6 x 7 8 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 0 1 2 3 4 5 6 7 8 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 .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 0 1 2 3 4 5 6 7 8 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 14 20 13 12 16 14 15 17 14 15 9 12 8 > 13 7 5 7 2 5 6 10 6 4 6 2 5 3 1 6 > 3 3 3 2 3 4 5 2 3 4 2 4 2 4 4 > 3 > Repl average number of exchanges: > Repl 0 1 2 3 4 5 6 7 8 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 .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. > -- > 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.
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