Re: looping on multiple dcds in namd configuration file

Date: Fri Nov 15 2019 - 00:59:51 CST

Dear Miro,

Thank you for your reply, but I know about catdcd. But my trajectory is quite large (about a 90 gb in total), and I have four trajectory like that. So I was thinking about avoiding to use catdcd, as even after merging the files, I have to upload the merged trajectory on the hpc for calculations (I don't have vmd installed on the hpc here). So I was thinking I can avoid all this if there is another way available.


From: Miro Astore <>
Sent: Friday, November 15, 2019 12:14 PM
To: Namd Mailing List <>; SHIVAM TIWARI <>
Subject: Re: namd-l: looping on multiple dcds in namd configuration file

If the files are not too large you can just
catdcd -o sum.dcd 1st.dcd 2nd.dcd 3rd.dcd 4th.dcd 5th.dcd

catdcd is located in vmd/plugins/LINUXAMD64/bin/catdcd5.1/catdcd

There are sometimes issues with the 1.9.3 version I have found so it is safer to use 1.9.2. Or you can use the animate plugin

To script loading of dcd files could look something like:

mol new molecule.psf
set list {"1st.dcd" "2nd.dcd" "3rd.dcd" "4th.dcd" "5th.dcd"}
for {set i 0} {i < [llength $list]} {incr i} {
set file [lindex $list $i]
mol addfile $file

is a ham fisted way of doing it I guess

On Fri, Nov 15, 2019 at 5:35 PM SHIVAM TIWARI <<>> wrote:
Dear namd users,

Let us say I have a 100 ns simulation which is divided into multiple dcds of 20 ns each dcd, how can I perform pair interaction calculation for the whole simulation (upto 100 ns) in a single run.
In other words , if there is a way to create a loop in the configuration file for pair interaction analysis, so that namd reads the dcds in the given sequence, and produces a single log file for the energies between the pairs upto 100 ns.


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