VMD-L Mailing List

From: Ackad, Edward (eackad_at_siue.edu)
Date: Thu Jan 16 2020 - 10:05:10 CST

Thank you!

On Thu, Jan 16, 2020 at 3:37 AM Paweł Kędzierski <pawel.kedzierski_at_pwr.edu.pl<mailto:pawel.kedzierski_at_pwr.edu.pl>> wrote:
W dniu 15.01.2020 o 20:23, Ackad, Edward pisze:
Hi all,
I'm trying to write a python script with minimal dependencies and that uses namdEneriy to calculate the energy of a dcd file. Is there a better way than externally calling vmd to load the psf+dcd and call namdEnergy from within vmd?
Have a look at the NAMD input script generated by NAMD Energy plugin and generate something similar in your Python code. It's minimalistic and the keywords are human readable, but of course you may find their description in NAMD User Guide in case of doubts. Then, run NAMD from Python. You will depend on NAMD only and also it will be much easier to debug than Python->VMD->plugin->NAMD approach. You will need also to parse the namd output yourself but this should be as easy as:


for line in open('Eint.log'):
    if line.startswith('ENERGY:'):
        energy = float(line.split()[13]) # POTENTIAL
        ...

HTH,
Pawel

Thanks!
Eddie

--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390



--
_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390