[gmx-users] Error in T-coupling of 2 atoms in T-couplingGroups

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 2 18:02:11 CEST 2008

Chitrita Duttaroy wrote:
> Thank you Justin and Sudheer.
> I had already made a solution to my problem, but didn't know whether it 
> was right. To confirm it I want to discuss it with you.
> After doing grompp to add Na+ to the water box I have done make_ndx with 
> .gro file. Then in the index file I merged the index no. of 2 [NA+] into 
> the [SOL] group and deleted the [NA+] group. After that I could do the 
> position restrained grompp with the file that 2 Na+ ions.

That's fine, but it is not necessary to delete the [NA+] group.  As long as a 
SOL_NA+ group is present, grompp will not complain.


> I want to know is it a correct method or not.
> Thanking you in advance,
> with regards


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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