<div dir="ltr"><div>Hi,</div><div> </div><div>There is nothing unique about an rdf from NPT. The box size is needed only to unwrap everything correctly. Use DCD for MD exclusively in the future. PDB is also an option but it's rather low precision. You can convert using Atomic Simulation Environment to a format readable by VMD that allows rdf with variable cells. </div><div> </div><div>My directory contains the files, <div style="background-color: rgb(250, 250, 250); border-color: rgb(187, 187, 187); border-style: solid; border-width: 1px; overflow-wrap: break-word;" class="prettyprint"><code class="prettyprint"><div class="subprettyprint">foo.cell foo-pos-1.xyz</div></code></div> </div><div>I generated random unit cell parameters with,</div><div><div style="background-color: rgb(250, 250, 250); border-color: rgb(187, 187, 187); border-style: solid; border-width: 1px; overflow-wrap: break-word;" class="prettyprint"><code class="prettyprint"><div class="subprettyprint">for ((i=0; i<310; i++)); do a=`echo "30 + $RANDOM/30" | bc`; b=`echo "30 + $RANDOM/30" | bc`; c=`echo "30 + $RANDOM/30" | bc`; echo "$i $i $a $b $c 90 90 90"; done > foo.cell</div></code></div></div><div> </div><div>In bash, $RANDOM is any 16-bit integer (ceil is 32767); I add 30 just in case $RANDOM is zero. I don't remember the exact format of the .cell file, so I took a guess of it as `step time, a, b, c, alpha, beta, gamma`. </div><div> </div><div>Here are some of the lines,</div><div><div style="background-color: rgb(250, 250, 250); border-color: rgb(187, 187, 187); border-style: solid; border-width: 1px; overflow-wrap: break-word;" class="prettyprint"><code class="prettyprint"><div class="subprettyprint">0 0 366 530 687 90 90 90 1 1 146 367 536 90 90 90 2 2 928 744 656 90 90 90 3 3 767 1043 943 90 90 90 4 4 621 932 711 90 90 90 5 5 854 1113 581 90 90 90 6 6 1033 204 505 90 90 90 7 7 1057 179 1028 90 90 90 8 8 222 944 814 90 90 90 9 9 552 339 296 90 90 90 10 10 381 807 488 90 90 90 11 11 1020 745 763 90 90 90 12 12 1121 126 34 90 90 90 13 13 802 552 413 90 90 90 14 14 388 1115 473 90 90 90 15 15 752 171 48 90 90 90 16 16 963 438 595 90 90 90 17 17 1039 374 766 90 90 90 18 18 858 514 198 90 90 90 19 19 970 710 161 90 90 90 20 20 175 505 992 90 90 90 </div></code></div> </div><div>Format doesn't matter, just needs to be in columns (with 2 buffer columns with step and physical time listed).</div><div> </div><div>And now a Python script for use with ASE, </div><div><div style="background-color: rgb(250, 250, 250); border-color: rgb(187, 187, 187); border-style: solid; border-width: 1px; overflow-wrap: break-word;" class="prettyprint"><code class="prettyprint"><div class="subprettyprint">#!/usr/bin/env python3 ''' usage: python3 xyzcell2gro.py Reads XMOL format file, adds lattice parameters, dumps Gromos file that can be read by VMD. ''' import glob import os import sys import numpy as np import ase from ase.io import read, write dir = os.getcwd() # trajectory is XMOL format # cell is step time a b c alpha beta gamma for file in glob.glob('%s/*-pos-*.xyz' % dir): filename, fileext = os.path.splitext(file) fileroot, filescrap = filename.split('-pos') trj = read('%s%s' % (filename, fileext) , format='xyz', index=':') cel = np.loadtxt('%s.cell' % (fileroot), usecols=range(2,8), dtype=np.double) nframes = len(trj) for frame in range(nframes): trj[frame].set_cell([ cel[frame][0], cel[frame][1], cel[frame][2], cel[frame][3], cel[frame][4], cel[frame][5] ]) trj[frame].set_pbc([True, True, True]) write('%s.g96' % (fileroot), trj[frame], format='gromos', append=True)</div></code></div></div><div> </div><div>The gromos format needs extension .g96 to be read by default in VMD. </div><div> </div><div>-T </div><div> </div><div> </div>On Wednesday, October 23, 2019 at 2:27:46 PM UTC-3, Ant wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">If anyone knows how to make RDFs for NPT simulation results that already exist, it would be great to know. </div></blockquote></div>