From: Fidan Sumbul (fidansumbul_at_gmail.com)
Date: Mon Nov 06 2017 - 11:11:28 CST
Dear NAMD users,
I run an MD equilibration, everything seems perfect except the atom indices in .coor files.
When I was trying to restart a continuing simulations i saw that the coor files is not written appropriately like in the part below. Do you have any idea what could be the reason of having this problem?
ATOM 19599 H2 TIP3W8978 -21.505 -14.565 16.296 1.00 0.00 WT8 H
ATOM 1959 OH2 TIP3W8984 -8.440 -9.959 303.081 1.00 0.00 WT8 O
ATOM 1959 H1 TIP3W8984 -7.847 -9.284 302.749 1.00 0.00 WT8 H
ATOM 1959 H2 TIP3W8984 -8.142 -10.120 303.976 1.00 0.00 WT8 H
ATOM 1959 OH2 TIP3W8988 -16.633 -0.772 259.331 1.00 0.00 WT8 O
ATOM 1959 H1 TIP3W8988 -16.634 -0.076 259.989 1.00 0.00 WT8 H
ATOM 1959 H2 TIP3W8988 -16.278 -1.534 259.789 1.00 0.00 WT8 H
ATOM 195 OH2 TIP3W8994 19.399 -20.651 397.430 1.00 0.00 WT8 O
ATOM 195 H1 TIP3W8994 18.728 -19.999 397.230 1.00 0.00 WT8 H
ATOM 195 H2 TIP3W8994 19.567 -20.545 398.366 1.00 0.00 WT8 H
ATOM 195 OH2 TIP3W9001 1.257 -1.078 402.300 1.00 0.00 WT8 O
ATOM 195 H1 TIP3W9001 0.470 -1.324 402.785 1.00 0.00 WT8 H
ATOM 195 H2 TIP3W9001 1.977 -1.255 402.906 1.00 0.00 WT8 H
ATOM 195 OH2 TIP3W9004 8.523 21.799 -17.381 1.00 0.00 WT8 O
ATOM 195 H1 TIP3W9004 9.365 22.032 -16.990 1.00 0.00 WT8 H
…
ATOM 19618 OH2 TIP3W9234 24.936 -0.275 349.858 1.00 0.00 WT8 O
ATOM 19619 H1 TIP3W9234 24.706 0.158 349.036 1.00 0.00 WT8 H
ATOM 1961 H2 TIP3W9234 24.350 -1.030 349.905 1.00 0.00 WT8 H
ATOM 1961 OH2 TIP3W9235 18.019 -13.473 360.731 1.00 0.00 WT8 O
ATOM 1961 H1 TIP3W9235 17.725 -14.272 360.294 1.00 0.00 WT8 H
ATOM 1961 H2 TIP3W9235 18.933 -13.375 360.463 1.00 0.00 WT8 H
ATOM 1961 OH2 TIP3W9241 23.147 6.036 116.004 1.00 0.00 WT8 O
ATOM 1961 H1 TIP3W9241 22.975 6.784 116.576 1.00 0.00 WT8 H
ATOM 19620 H2 TIP3W9241 24.010 6.214 115.629 1.00 0.00 WT8 H
ATOM 19621 OH2 TIP3W9250 20.174 5.935 258.046 1.00 0.00 WT8 O
ATOM 19622 H1 TIP3W9250 20.359 6.627 257.411 1.00 0.00 WT8 H
Best,
Fidan Sumbul, PhD
Postdoctoral Researcher
U1006 INSERM
Parc Scientifique et Technologique de Luminy
Bâtiment Inserm TPR2 bloc 5
163 avenue de Luminy
13009 Marseille
France
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