Hi,
You might be able to get what you want with a for loop. Something like:
set masks = '":PC.P31" ":PC.N31" ":PC.C2" ":PC | :OL | :OL2"'
set del = 'delta 0.25'
set out1 = number_density.dat
parm ../DOPC.parm7
trajin ../DOPC.rst7
# Set MAX to the current number of frames
set MAX = trajinframes
# Clear the trajectory
clear trajin
# Loop over each frame individually, calculate density
for i=1;i<=$MAX;i++
# Load only the desired frame
trajin ../DOPC.rst7 $i $i
center ":PC | :OL | :OL2" origin
density out $out1.$i number $del $masks name frame.$i
# Clear that frame
clear trajin
done
Hope this helps,
-Dan
On Tue, May 11, 2021 at 2:03 PM ARITRA MITRA <aritra18.iitg.ac.in> wrote:
>
> Dear Amber Users,
> This query is regarding the 'density' analysis in CPPTRAJ. I am running the following script in order to obtain the density distribution of water as a function of box length in the x direction.
>
> parm abc.prmtop
> trajin abc.crd
> density out wat-density-x.dat name x-axis-wat delta 0.1 x mass :WAT
>
> The output file contains the density values averaged over the entire trajectory (along with the standard deviation values) . For the purpose of my analysis, I wish to calculate the
> density values per frame such that in addition
> to the box length and density data the time information will also be written out. I need a workaround to bypass the time average feature of the 'density' keyword. Any suggestion on this
> topic is highly appreciated.
> Thanks in advance.
>
>
>
> Regards,
>
> Aritra Mitra,
>
> Senior Research Fellow,
>
> Prof. Sandip Paul's Group,
>
> Department of Chemistry,
>
> IIT Guwahati.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue May 11 2021 - 12:30:02 PDT
