From: Miro Astore (miro.astore_at_gmail.com)
Date: Fri Nov 15 2019 - 05:22:34 CST
There is also bigdcd which can read one frame at a time and just loops
through arbitrary length files.
https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/
On Fri., 15 Nov. 2019, 17:59 SHIVAM TIWARI, <t.shivam_at_iitg.ac.in> wrote:
> 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.
>
> regards
> shivam
>
> ------------------------------
> *From:* Miro Astore <miro.astore_at_gmail.com>
> *Sent:* Friday, November 15, 2019 12:14 PM
> *To:* Namd Mailing List <namd-l_at_ks.uiuc.edu>; SHIVAM TIWARI <
> t.shivam_at_iitg.ac.in>
> *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
> https://www.ks.uiuc.edu/Research/vmd/current/ug/node121.html
>
> 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 <t.shivam_at_iitg.ac.in> 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.
>
>
> regards
> shivam
>
>
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