From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Fri Jun 21 2019 - 11:27:15 CDT
I am not an expert on the internals of the minimizer in NAMD, but is it
possible that it has a heuristic that "walks back" if it notices an
increase in energy?
It looks like the energies Pawel is getting in between repeated coordinates
are higher in energy, then it "re-sets" to a previous coordinate set that
had lower energy and tries again.
The QM-Only DCD writes the exact coordinate that NAMD is sending for QM
calculations, so somehow NAMD is producing the exact same coordinates.
On Fri, 21 Jun 2019 at 08:01, Pawel Kedzierski <pawel.kedzierski_at_pwr.edu.pl>
> W dniu 20.06.2019 o 16:46, Marcelo C. R. Melo pisze:
> 2) How are you checking the coordinates sent to the QM software? Are you
> saving a DCD at every step?
> I have confirmed that the coordinates saved by NAMD in the QM-only DCD
> file are repeated every few steps.
> Python code used to check this is pasted below.
> 3) I noticed you are using the NAMD build from Nov/2018. (NAMD 2.13 for
> Linux-x86_64-multicore, Built Fri Nov 9 14:39:16 CST 2018 by jim on
> Do you have access to a new one? Could you download the pre-compiled one
> from the NAMD website for tests?
> Downloaded and tested this binary build:
> NAMD Git-2019-06-21 for Linux-x86_64-multicore
> Based on Charm++/Converse 60800 for multicore-linux64-iccstatic
> Built Fri Jun 21 02:03:40 CDT 2019 by jim on belfast.ks.uiuc.edu
> Same problem.
> Best regards,
> Paweł Kędzierski
> #!/usr/bin/env python3
> # Load coordinates from DCD trajectory and compare them. Requires catdcd,
> # Python >=3.5 and numpy Python library
> # Arguments: file.psf file.dcd
> import numpy as np, subprocess as sp, sys
> inpsf, indcd = sys.argv[1:3]
> sp.run(['catdcd', '-o', 'tmp.xyz', '-otype', 'xyz', '-s', inpsf,
> '-stype', 'psf', indcd], check=True, stdout=sp.PIPE)
> prec = None
> frames = 
> with open('tmp.xyz', 'r') as xyz:
> for line in xyz:
> words = line.split()
> if len(words)==1: # the line with atom count
> natoms = int(words)
> next(xyz) # skip comment
> coords = np.zeros((natoms,3), dtype=float) # array for coordinates
> for i in range(natoms):
> words = next(xyz).split()
> if not prec: # recognize precision of coords in xyz file
> prec = len(words.split('.'))
> coords[i] = words[1:4] # read x,y,z line by line
> frames.append(coords) # remember this frame of coordinates
> N = len(frames)
> print("\nSuccessfully read %d frames with precision to the %d'th decimal point."
> % (N, prec))
> # Now, compare the frames
> eps = eval('1e-%d' % prec)
> found = False
> for i in range(N-1):
> anynew = False
> for j in range(i+1, N):
> if np.all(np.abs(frames[i] - frames[j]) < eps):
> if not found:
> print('Pairs of identical frames (0-based indices):')
> found = True
> anynew = True
> print('%d-%d' % (i,j), end=' ')
> if anynew:
> print() # flush line
> if not found:
> print('None of the frames were identical.')
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