From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Fri Jun 21 2019 - 07:01:03 CDT
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 ganymede.ks.uiuc.edu <http://ganymede.ks.uiuc.edu/>)
> 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[0])
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[1].split('.')[1])
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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