Hi all,
My system contains water (SOL) + polyelectrolyte (PSS with DP 30) +
sodium ions (Na). Before the EM, I have run "editconf -f -noc -resnr 1
-o" to set the resnr. After the EM, the resnr becomes wrong. But the
atomnr is still correct.
1. the resnr of the first water starting from "DP+1", not 1. (I have
checked some other systems with DP=15 or DP=12)
2. the resnr of the first PSS residue on the ALL the PSS chain starts
from 1, but not the resnr(of previous water/PSS residue) +1.
3. the resnr of the first Na residue is the resnr(of the last water
residue) +1, but not the resnr(of the previous PSS residue) +1
It seems that the problem is caused from the polymer. Any comment or
suggestion is sincerely welcome!
Gromacs 4.5.3
************************************************
0.1MNaCl + DP30
380329
31SOL OW 1 4.323 10.990 14.598 -0.2147 0.1640 -0.0659
31SOL HW1 2 4.280 11.043 14.525 -0.8319 3.1315 2.3305
31SOL HW2 3 4.253 10.953 14.659 0.3787 -0.3030 0.3439
32SOL OW 4 0.863 3.787 10.720 0.8624 -0.6556 0.5765
32SOL HW1 5 0.785 3.827 10.671 1.9981 0.4779 -0.3465
32SOL HW2 6 0.904 3.716 10.663 0.9971 -0.6900 0.7175
........................
......................
99316SOL OW97856 0.834 8.769 22.747 -0.2436 -0.7048 0.2608
99316SOL HW197857 0.931 8.745 22.754 -0.0076 0.0674 -0.2549
99316SOL HW297858 0.819 8.860 22.787 -0.9561 -1.2962 1.3663
1PSS CAA97859 9.971 3.747 8.913 0.0608 -0.0677 -0.0792
1PSS HAA197860 9.949 3.849 8.936 0.1767 -0.4602 1.7875
.....................
30PSS HAB298430 8.204 6.232 10.780 0.9449 -0.2721 0.7855
1PSS CAA98431 1.197 5.317 19.589 -0.1509 -0.1143 -0.2474
.........................
30PSS HAB299002 1.549 1.832 20.579 1.3918 3.3370 1.4906
1PSS CAA99003 5.657 5.376 6.520 -0.1073 -0.0351 -0.8729
...........................
30PSS HAB2 9298 3.526 0.458 16.652 -1.6044 1.1441 1.3393
99317Na Na 9299 12.146 5.676 14.924 -0.1802 -0.9861 0.2229
99318Na Na 9300 11.363 11.645 8.887 0.4524 -0.4644 -0.0401
...........................
..............................
************************************************
regards,
Baofu Qiao
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