From: Prathit Chatterjee (
Date: Thu Dec 23 2021 - 09:08:51 CST

Thank you Prof. Kohlmeyer for the clarification.

    On Thursday, 23 December, 2021, 10:22:35 pm GMT+9, Axel Kohlmeyer <> wrote:

On Thu, Dec 23, 2021 at 6:37 AM Prathit Chatterjee <> wrote:

Dear Experts,Kindly let me know how to write a netcdf file with VMD from a netcdf/dcd trajectory file.It seems that VMD can read a netcdf file but cannot write it, as follows:

That is correct. In order to be able to write a trajectory in a given format the corresponding plugin must have write support functions included.The NetCDF plugin does not have them just like many other molfile plugins. From the source code:
$ grep '\.open_file_write' molfile_plugin/src/*.{c,C} | wc -l
$ grep '\.open_file_read' molfile_plugin/src/*.{c,C} | wc -l

so only 24 out of 84 molfile plugins do support writing files.
Info) Using plugin netcdf for coordinates from file /data1/Prathit/APP/OnlyAPP/AlphaFold2/770_res/Charmm-Gui_Dimer-units/E1-E1_3189357573/windows/smd.10_image.ncInfo) Coordinate I/O rate 139.6 frames/sec, 470 MB/sec, 3.6 secInfo) Finished with coordinate file /data1/Prathit/APP/OnlyAPP/AlphaFold2/770_res/Charmm-Gui_Dimer-units/E1-E1_3189357573/windows/ >vmd > molinfo top get numframes500vmd > set nf [expr {[molinfo top get numframes]-1}]499vmd > set all [atomselect top all]atomselect1vmd > animate write dcd try.dcd beg 0 end $nf waitfor all sel $allInfo) Opened coordinate file try.dcd for writing.Info) Finished with coordinate file try.dcd.500vmd >vmd > animate write netcdf beg 0 end $nf waitfor all sel $allERROR) Unable to open file of type netcdf for writing frames.vmd >vmd > animate write netcdf type netcdf beg 0 end $nf waitfor all sel $all (basically it did not write an .nc file, unlike the generated .dcd file above)vmd > lsAny comments regarding the same will be deeply appreciated.Thanks in advance.Prathit Chatterjee

Dr. Axel Kohlmeyer;!!DZ3fjg!plEMYRmD5WZmZSUWnkd4nqk1wSqf_dNTqscdfrK_9R4bH78lAzYI2uufCRX041NR8w$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.