[gmx-users] unable to understand dPCA

[Seera Suryanarayana]

Dear gromacs users,

I have done simulations of 20 residues length peptide for 300ns. As I would
like to do explore the conformational space I have chosen the dPCA to find
flexible regions. I have gone through the dPCA tutorial from gromacs site
and followed it. First I have generated the index file by mk_angndk and I
got following index file and I have chosen zero group (top one).

[ Phi=180.0_2_43.93 ]
     5    25    23    24    27    47    45    46    49    69    67    68
    71    88    86    87    90    99    97    98   101   121   119   120
   123   131   129   130   133   143   141   142   135   139   138   140
   145   162   160   161   164   169   167   168   171   179   177   178
   180   193   191   192   195   204   202   203   206   211   209   210
   213   231   229   230   233   253   251   252   255   270   268   269
   272   286   284   285   288   297   295   296   299   313   312   314

[ Phi=180.0_2_4.18 ]
    23    27    25    26    45    49    47    48    67    71    69    70
    86    90    88    89    97   101    99   100   119   123   121   122
   129   133   131   132   141   145   143   144   160   164   162   163
   167   171   169   170   177   180   179   188   191   195   193   194
   202   206   204   205   209   213   211   212   229   233   231   232
   251   255   253   254   264   262   266   267   268   272   270   271
   284   288   286   287   295   299   297   298   308   306   310   311

[ Phi=180.0_2_4.60 ]
   215   218   221   219   218   223   219   220   218   225   221   222
   219   227   223   224   221   227   225   226   223   225   227   228
   257   260   262   261   260   266   262   263   261   266   264   265
   301   304   306   305   304   310   306   307   305   310   308   309

Then I have to get another index file which tells to the trjconv to
generate .gro file. Here I am unable to generate index file. As I want
create complete complete peptide .gro file except both terminal residues.
Based on the 2*N/3 formula, it is not possible to create complete .gro
file. Kindly tell how to create complete gro file for peptide of my
interest.

Thanks in advance
Surya
Graduate student
India.