[gmx-users] Re: freeze the particular residues in NPT-NVT

[라지브간디]

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Dear Justin,


I have checked my index.ndx file and it doesnt have any atoms close to 37872 atoms. I am bit confused why its happening. 




Contents of index file fz.ndx
--------------------------------------------------
Nr.   Group               #Entries   First    Last
   0  System                  2124       1    2124
   1  Protein                 1522       1    1522
   2  Protein-H               1204       1    1522
   3  C-alpha                  151       5    1506
   4  Backbone                 453       1    1520
   5  MainChain                605       1    1522
   6  MainChain+Cb             746       1    1522
   7  MainChain+H              754       1    1522
   8  SideChain                768       6    1519
   9  SideChain-H              599       6    1518
  10  Prot-Masses             1522       1    1522
  11  non-Protein              602    1523    2124
  12  Other                     59    1523    1581
  13  SO4                       10    1523    1532
  14  HEM                       47    1533    1579
  15  CMO                        2    1580    1581
  16  Water                    543    1582    2124
  17  SOL                      543    1582    2124
  18  non-Water               1581       1    1581
  19  g1                        10      28      37
  20  g2                        12      74      85
  21  g3                        12     241     252
  22  g4                        17     289     305
  23  g5                        10     400     409
  24  g6                        17     423     439
  25  g7                        17     449     465
  26  g8                        17     466     482
  27  g9                        13     483     495
  28  g10                        9     508     516
  29  g11                       13     574     586
  30  g12                        9     620     628
  31  g13                       13     642     654
  32  g14                       12     655     666
  33  g15                       12     897     908
  34  g16                       13     944     956
  35  g17                       10    1091    1100
  36  g18                        9    1145    1153
  37  g19                       12    1154    1165
  38  g20                        8    1166    1173
  39  g21                       17    1174    1190
  40  g22                        9    1254    1262
  41  g23                       12    1269    1280
  42  g24                       13    1312    1324
  43  g25                       10    1340    1349
  44  g26                       17    1359    1375
  45  g27                        9    1415    1423
  46  g28                       18    1449    1466
  47  g29                       19    1504    1522





> 
Usually the "Protein Non-Protein" approach covers everything. Apparently in 
your case, something is wrong and you will have to figure out what has not 
been accounted for. Try using gmxcheck on your index file to see if there 
is a group (or groups) whose contents account for 37872 atoms. 

-Justin