Dear Dan,
I am following your code but ending up with syntax errors. Here is a sample of the code I am running:
set out1 = number_density.dat
set del = 'delta 0.1'
set mask = '":OLA| :LQZ"'
parm des-50-wat-50-253K.prmtop
trajin des50-pd-1076ns.nc
set MAX = trajinframes
clear trajin
for i=1;i<=$MAX;i++
trajin des50-pd-1076ns.nc $i $i
center $mask origin
density out ./out_files/$out1.$i number $del $mask name frame.$i
clear trajin
done
The error I am getting is as follows:
[for i=1;i<=1000;i++]
Setting up 'for' loop.
Error: End argument must be an integer.
1 errors encountered reading input.
I am not sure as to where I am going wrong. I have looked up the usage of for loops in CPPTRAJ and I can't figure out the error in my code.
I am using AmberTools19. Can you please help me out?
Regards,
Aritra Mitra,
Senior Research Fellow,
Prof. Sandip Paul's Group,
Department of Chemistry,
IIT Guwahati.
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: 12 May 2021 00:39
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again.
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 Thu May 13 2021 - 08:00:02 PDT
