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decaalanine
dppc_mapping
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README
dopc.itp
dppc.itp
extract.1aa.seq.sh
gen_energygrp.sh
gen_ndx.sh
nb_generic_cg-GMX-4.5.4_5.c
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nb_generic_cg-GMX-4.6.6.c
nb_generic_cg-GMX-4.6.6.patch
pdb2gro.sh
pdb_aa2cg.no_vmd.sh
pdb_aa2cg.sh
plum.itp
plum_prot_gen_itp.pl
popc.itp
source.me

README

Tristan Bereau, Aug. 9, 2011.


                    PLUM forcefield in Gromacs
                          Deserno group
            Dept. of Physics, Carnegie Mellon University
                  Pittsburgh, PA 15232, USA

References:
==========

 * Lipid force field: 
[1] Z.-J. Wang and M. Deserno, J. Phys. Chem. B 184, 351-363 (2010).

 * Peptide force field: 
[2] T. Bereau and M. Deserno, J. Chem. Phys. 130, 235106 (2009).

 * Protein-Lipid interactions:
[3] T. Bereau, Unconstrained Structure Formation in Coarse-Grained Protein
               Simulations, Chapter 6, Ph.D. thesis (2011)


Gromacs Setup:
=============

Please note that the following steps are NOT necessary if you want to use the
Lipid force field [1] alone. The special kernel is needed for the Peptide [2] and the
Protein-Lipid part [3] of the force field.

in case of Gromacs 4.5.5:

 * Replace the charge-group--charge-group kernel to add an implementation of
   he hydrogen-bond interaction as described in [1]. 
   To do so one can either apply the nb_generic_cg.c.patch to your gromacs source:

   cd path/to/gromacs
   patch -p1 <nb_generic_cg.c.patch

   or replace the charge-group--charge-group kernel in
   src/gmxlib/nonbonded/nb_generic_cg.c by the file included in this archive.

 * recompile Gromacs

in case of Gromacs 4.5.4:

 * In the Gromacs directory, replace the charge-group--charge-group kernel
   src/gmxlib/nonbonded/nb_generic_cg.c by the file included in this archive.
   It contains the implementation of the hydrogen-bond interaction as
   described in [1].

 * In the Gromacs directory, open src/mdlib/ns.c.  Around line 322, comment
   out the line:
     
    gmx_fatal(FARGS,"The charge-group - charge-group force loops only \
     support systems with all intra-cg interactions excluded and no inter-cg \
     exclusions, this is not the case for this system.");

   This problem has been solved in Gromacs 4.5.5 and above.

 * recompile Gromacs

Simulation setup:
================

 * Copy plum_tables/*.xvg into simulation directory.

 * Write protein sequence file protein.seq: 1 protein per line, all 1-letter
   amino acid codes, no spaces between letters.  Example: 15-residue
   polyalanine:

   AAAAAAAAAAAAAAA

   See also WALP peptide in example directory: popc72_walp/walp.seq.  Special
   amino acid codes:
   - Z: end cap (N-terminal or C-terminal group)
   - B: Arginine [+]; (neutral arginine is R)
   - J: Aspartic acid [-]; (neutral aspartic acid is D)
   - O: Glutamic acid [-]; (neutral glutamic acid is E)
   - U: Lysine [+]; (neutral lysine is K)

 * Copy lipid force field file(s) (i.e., {dopc,popc,dppc}.itp) and plum.itp to
   simulation directory.

 * Generate protein force field file by using script:
   
   ./plum_prot_gen_itp.pl protein.seq > prot.itp

 * Write topology file topol.top which combines the lipid, protein, and plum
   .itp files.  (See example file: popc72_walp/topol.top).

 * Generate .gro file from a pdb structure which contains the lipid and
   protein coordinates (concatenated) from the script

   ./pdb2gro.sh initial.pdb Lx Ly Lz

   where initial.pdb is the pdb structure, and Lx, Ly, and Lz are the three
   box sizes (in nm) in the x, y, and z directions, respectively.

   Note 1: an atomistic protein can simply be coarse-grained by using the
   script 

   ./pdb_aa2cg.sh protein.pdb

   Note 2: pdb2gmx does _not_ work with PLUM because the residue database has
   not yet been implemented (see .rtp files in the Gromacs manual).

 * Copy grompp.mdp file from example directory popc72_walp.  Use the script

   ./gen_energygrp.sh protein.seq 

   to generate 'energygrps' and 'energygrp_table' variables.  Insert script
   output in grompp.mdp file.  Make sure the 'userint{1,2,3}' variables are
   set as in the popc72_walp example (they are required for proper Hbond
   calculation).  Also, do not change the order of [atomtypes] in plum.itp
   file (the userint{2,3} variables correspond to the atomtypes of beads HBN
   and HBC, hydrogen-bonding capable amide and carbonyl groups).

 * Generate index file index.ndx from .gro file:

   ./gen_ndx.sh conf.gro

 * Export environment variable GMX_NBLISTCG (see file 'source.me') to activate
   charge-group--charge-group kernel (this includes the Hbond interaction):

   source source.me

   Note: in case of lipid-only simulation (i.e., no protein), it is best _not_
   to export GMX_NBLISTCG (or, alternatively, to set as 0) which is only
   required when the charge-group--charge-group kernel needs to use the C code
   (i.e., where the Hbond interaction is implemented).  This will speed up
   performance. 

 * The grompp command requires the following files: mdp, gro, top, ndx, and
   the option -norenum to prevent reordering of the atomtypes (because of the
   Hbond potential):

   grompp -f grompp.mdp -c conf.gro -p topol.top -n index.ndx -norenum

   Note: the example directory popc72_walp contains all the necessary files
   for a PLUM simulation in Gromacs of that system.

 * mdrun -v