[gmx-users] residue number starting from not 1

[Baofu Qiao]

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