[gmx-users] Freezing part of a structure

[Darrell Koskinen]

Dear GROMACS Gurus,
I tried to freeze two ends of a graphene structure (Grph) by assigning 
the HA atoms, at two ends of the graphene lattice, their own residue 
name (Frze) and residue number (210) in the .gro file. Before the 
assignment, the HA atoms belonged to the same residue as the CA atoms. 
Here is a section of my .gro file:

      1Grph CA    4836  31.390   6.800   5.000  0.0000  0.0000  0.0000
      1Grph CA    4837  31.390   7.040   5.000  0.0000  0.0000  0.0000
      1Grph CA    4838  31.390   7.280   5.000  0.0000  0.0000  0.0000
      1Grph CA    4839   6.610   7.280   5.000  0.0000  0.0000  0.0000
*  210Frze HA    5116   6.510   7.280   5.000  0.0000  0.0000  0.0000*
      1Grph CA    4840   6.610   7.040   5.000  0.0000  0.0000  0.0000
*  210Frze HA    5117   6.510   7.040   5.000  0.0000  0.0000  0.0000*
      1Grph CA    4841   6.610   6.800   5.000  0.0000  0.0000  0.0000

I then run the .gro file through x2top and get the following:
  5072   opls_145     13   Grph     CA   4836          0     12.011   ; 
qtot 0
  5073   opls_145     13   Grph     CA   4837          0     12.011   ; 
qtot 0
  5074   opls_145     13   Grph     CA   4838          0     12.011   ; 
qtot 0
  5075   opls_145     13   Grph     CA   4839      -0.06     12.011   ; 
qtot -0.06
*  5076   opls_146     14   Frze     HA   4839       0.06      1.008   ; 
qtot 0*
  5077   opls_145     15   Grph     CA   4840      -0.06     12.011   ; 
qtot -0.06
*  5078   opls_146     16   Frze     HA   4840       0.06      1.008   ; 
qtot 0*
  5079   opls_145     17   Grph     CA   4841      -0.06     12.011   ; 
qtot -0.06

It appears that the residue numbers have been re-assigned by x2top. Is 
this causing a problem, since when I run these .gro files and .top files 
through grompp & mdrun once for EM and then once again for MD, I get the 
correct number of atoms in the .gro file produced by the EM mdrun but 
get almost double the amount of atoms in the .gro file produced by the 
MD mdrun?

Thanks again for your help.

Darrell