[gmx-users] Freezing part of a structure

[Justin A. Lemkul]

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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-- 
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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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