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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
What steps will reproduce the problem?
just follow the steps in https://code.google.com/p/plumx/wiki/helloWorld
or https://code.google.com/p/plumx/wiki/helloWorldPep
What is the expected output? What do you see instead?
The Ala 10-mer should stay a helix but it unfolded;
The membrane-peptide simulation just crashed
What version of the product are you using? On what operating system?
gromacs 4.6.6; Fedora 18;
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 20 Nov 2014 at 3:46
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