Dear Dan,
The CPPTRAJ version I am currently using is:
CPPTRAJ: Version V4.14.0 (AmberTools V19.00)
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: 13 May 2021 20:32
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again.
Hi,
What Version of CPPTRAJ are you using? You may need the latest from GitHub
for the <= operator to work.
-Dan
On Thu, May 13, 2021 at 10:34 AM ARITRA MITRA <aritra18.iitg.ac.in> wrote:
> 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 - 08:30:03 PDT
