|
Hi all.
1) 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. 2)
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. |
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
