[gmx-users] how to apply distance restrains between a residue and an ion
victordsmagift at gmail.com
Tue Sep 1 20:54:45 CEST 2015
I need to apply a distance restraint between a sodium and a residue. I read
the manual, etc, which seems to suggest adding something like below to the
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
10 16 1 0 1 0.0 0.3 0.4 1.0
10 28 1 1 1 0.0 0.3 0.4 1.0
But my protein and ions are in two separate itp file. So how do I do it?
Also I have multiple sodiums, but in the SOD.itp file, there is only one line
[ moleculetype ]
; name nrexcl
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 SOD 1 SOD SOD 1 1.000 22.9898
; qtot 1.000
So how do I get the atom number for the specific sodium I want to restraint?
Thank you so much.
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