Darrell Koskinen wrote:
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?
I have no idea why that would be happening; post your .mdp to see if there are
any clues, especially in the output options. It is really a lot easier to just
use make_ndx to create an index group with the atoms you want to freeze. No
special processing or re-numbering necessary; use your original .top and .gro files.
-Justin
Thanks again for your help.
Darrell
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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