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

[Justin Lemkul]

On 3/21/13 2:12 AM, 라지브간디 wrote:
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> Dear Justin,
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> I have checked my index.ndx file and it doesnt have any atoms close to 37872 atoms. I am bit confused why its happening.
>

There is some colossal mismatch between your coordinates, topology, and/or index 
file.  I would recommend eliminating all the freezing and special groups and try 
to get a vanilla system working, then add complexity with the groups you're 
trying to freeze.  There's something more fundamentally wrong here that you need 
to be solving first.

-Justin

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> 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
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>>
> 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
>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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