Re: Bug in NAMD

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Fri Jun 21 2019 - 11:27:15 CDT

Hi All,
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.

Best,
Marcelo

On Fri, 21 Jun 2019 at 08:01, Pawel Kedzierski <pawel.kedzierski_at_pwr.edu.pl>
wrote:

> 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)
> 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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