Hi all,
FYI I've implemented a new keyword for the 'hbond' command, 'splitframe',
that allows the average hbond output to be partitioned out into different
sections of the input trajectory. It is available in version 6.2.9 from
GitHub.
For example, 'splitframe 250,500,1000' will divide analysis into frames
1-249, 250-499, 500-999, and 1000 to end. So say you have two trajectories
that are 10000 frames each. You could load both in, then specify
'splitframe 10000' to the hbond command to have the results partitioned at
frame 10000, e.g.
trajin traj1.nc
trajin traj2.nc
hbond HB out nhb.dat avgout hbavg.dat splitframe 10000
I've also added the ability to track solute-solvent hydrogen bond bridges
vs time via the 'bseries' (and 'bseriesfile') keyword (analogous to
'series' for hydrogen bonds).
Both of the new keywords are fully functional in parallel. For more info,
see: https://github.com/Amber-MD/cpptraj/pull/948
Hope this is helpful,
-Dan
On Mon, Feb 14, 2022 at 7:23 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Right now, something like what Kenneth has done is probably the best way.
> However I have some ideas on this to make it simpler, and hope to implement
> them soon so stay tuned!
>
> -Dan
>
> On Mon, Feb 14, 2022 at 2:09 PM Kenneth Huang <khuang8.student.gsu.edu>
> wrote:
>
>> Hi,
>>
>> Not exactly a built in solution (think it involves readdata after you've
>> run the hbond, but someone else may remember more than me) but here's a
>> bash script I made a while back to brute force a comparision from the
>> hbond_avg output-
>> #print out from input to temp in range- make sure to have range defined
>> to avoid solute solvent hbond
>> awk 'NR>1 && NR<279 {print $1,$3,$5}' hbond_avg.*.out | awk '$3 > .05
>> {print ;}' > test
>>
>> #parse out the weird name to just res #, percent, and remove duplicate
>> entries
>> awk -F"_" '$1=$1' OFS=" " test | awk -F"." '$1=$1' OFS="\t" | awk '{print
>> $2,$5,$7}' | awk '!_[$1,$2]++' > test2a
>>
>> #have to do two passes for this part- won't work on first pass, so run
>> over other hbond_avg output for other traj to compare
>>
>> #match by col 1+2
>> awk 'FNR==NR{a[$1,$2];b[$1,$2];next} (($1,$2) in a) || (($1,$2) in b) '
>> test2a test3
>> It's rough and you may have to fiddle with it, but it might be a useful
>> start.
>>
>> Best,
>>
>> Kenneth
>>
>> ________________________________
>> From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
>> Sent: Monday, February 14, 2022 1:44 PM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: [AMBER] CPPTRAJ, Comparing H-bonding in two trajectories
>>
>> Dear Amber Community,
>>
>> Is there a built-in way to compare the H-bonding in two difference
>> trajectories to see how many are the same and how many are different (i.e.,
>> involve the same/different donor and acceptor pairs)?
>>
>> Best,
>> Matthew
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Received on Wed Feb 16 2022 - 13:00:02 PST
