mkolin at iimcb.gov.pl
Fri Mar 24 14:31:01 CET 2006
Thank you all for comments and help on FEP issue.
I still have problems with setting up the system.
How can I obtain topology for DPPC lipids to use with GROMOS96
force field for protein membrane simulations. Should I
stay with old ffgmx force field, is it the best choice.
Is it possible to adopt old lipid parameters (lipid.itp
for ffgmx) for new GROMS96 force field.
During FEP calculations I need to
slowly turn off charges and LJ interactions for Zn2+ ion.
In my dual topology for Zn2+ I have:
[ moleculetype ]
; molname nrexcl
[ atoms ]
; id at type res nr residu name at name cg nr charge typeB chargeB massB
1 Zn 1 Zn Zn 1 2 65.37000 Zn (?) 0 0
and that will only perturbate charges on the Zn atom.
In order to turn off Zn ion LJ interactions I need to
change it into dummy atom. I'm using ffgmx forcefield and
which atom type should I use for above Zn(?). I checked
ffgmx.atp and there is no atom type DUM (like in GROMOS96).
Does it mean I have to add new atom type DUM in all ffgmx.atm,
ffgmxnbon.itp.. files. Please give my some suggestions.
Thank you for your time and help.
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