Dear Users:
Sumary: Am I correct to presume that when running with pmemd the times
listed by "TIME(PS)=" in the .out file match up with the frames listed in
analyses output from cpptraj based on the .mdcrd trajectory file for
irest=1 but that when irest=0 there is an additional value of "TIME(PS)="
listed in the .out file for the very first frame that is not written out to
the .mdcrd trajectory file?
Detail: I have some pmemd runs that I have run in segments, either due to
wallclock limits or in recovery from a crash. I am having trouble figuring
out how to match the frames to timesteps. To try to figure this out, I have
started from the assumption that the value of time given for the
"TIME(PS)=" entry in the .out file corresponds to the tile of each frame in
the .mdcrd trajectory file. However, this does not seem to be the case. For
instance, I have a file called v12.out that has 745 "TIME(PS)=" entries
running from 0 to 743999.998, whereas when I analyze the v12.mdcrd file I
get output for only 744 frames. The number of times do match up with the
number of frames for restarts but just not on the first segment. So I
presume that the frame at TIME(PS)=0 is not saved for irest=0 but the first
frame listed as TIME(PS)= in the .out file is indeed saved when irest=1 ?
### Here is the script that I used to evaluate this:
for i in v12 v12_2 v12_3; do
numt=$(cat ${i}.out |grep "TIME(PS)"|sed "s/=/ /g"|awk '{print $4}'|wc -l)
mint=$(cat ${i}.out |grep "TIME(PS)"|sed "s/=/ /g"|awk '{print $4}'|head
-n 1)
maxt=$(cat ${i}.out |grep "TIME(PS)"|sed "s/=/ /g"|awk '{print $4}'|tail
-n 1)
rm -f tmp.out
{
cpptraj -p this.prmtop -y ${i}.mdcrd << EOF
nativecontacts name tAB mindist distance 6.0 out tmp.out :1-20 :41-60
go
EOF
} > /dev/null 2>&1
numf=$(cat tmp.out|grep -v "^#Frame" |wc -l)
minf=$(cat tmp.out|grep -v "^#Frame" |head -n 1|awk '{print $1}')
maxf=$(cat tmp.out|grep -v "^#Frame" |tail -n 1|awk '{print $1}')
echo nam=$i NUM_TIMES=$numt MIN_TIME=$mint MAX_TIME=$maxt
NUM_FRAMES=$numf MIN_FRAME=$minf MAX_FRAME=$maxf
rm -f tmp.out
done |column -t > test.output
##############################################
### Here is the output:
nam=v12 NUM_TIMES=745 MIN_TIME=0.000 MAX_TIME=743999.998
NUM_FRAMES=744 MIN_FRAME=1 MAX_FRAME=744
nam=v12_2 NUM_TIMES=44 MIN_TIME=744999.998 MAX_TIME=787999.998
NUM_FRAMES=44 MIN_FRAME=1 MAX_FRAME=44
nam=v12_3 NUM_TIMES=316 MIN_TIME=788999.998 MAX_TIME=1103999.994
NUM_FRAMES=316 MIN_FRAME=1 MAX_FRAME=316
### And here is output from a different set of continuations for a
different simulation:
nam=v8 NUM_TIMES=134 MIN_TIME=0.000 MAX_TIME=133000.000
NUM_FRAMES=133 MIN_FRAME=1 MAX_FRAME=133
nam=v8_2 NUM_TIMES=176 MIN_TIME=133000.000 MAX_TIME=308000.000
NUM_FRAMES=176 MIN_FRAME=1 MAX_FRAME=176
nam=v8_3 NUM_TIMES=44 MIN_TIME=309000.000 MAX_TIME=352000.000
NUM_FRAMES=44 MIN_FRAME=1 MAX_FRAME=44
nam=v8_4 NUM_TIMES=322 MIN_TIME=353000.000 MAX_TIME=673999.999
NUM_FRAMES=322 MIN_FRAME=1 MAX_FRAME=322
Thank you for your help,
Chris.
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Received on Tue Jan 17 2017 - 10:30:03 PST
