[gmx-users] FEP

Michal Kolinski mkolin at iimcb.gov.pl
Fri Mar 24 14:31:01 CET 2006

Hi all.

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
ZnB              1

[ 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.
All best.
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