To run the sample simulations:
$CHARMMEXEC < INPUTSCRIPT_FILENAME > LOG_FILENAME
or (tee bifurcates the output to screen and file),
$CHARMMEXEC < INPUTSCRIPT_FILENAME | tee LOG_FILENAME
1. GBSW implicit solvent simulation of protein G B1 domain
This example illustrates the usage of GBSW implicit solvent
simulation of a small protein. Several key differences from a
typical explicit water simulation exist.
- GBSW-specific CMAP: the peptide backbone torsion potentials have
been optimized consistently with the input radii for GBSW to accurately
describe peptide conformational equilibria.
read rtf card name @toppar/top_all22_prot_cmap.inp
read para card name @toppar/par_all22_prot_gbsw.inp
- Nonbonded interactions: no need to setup periodic boundary
conditions (unless you have good reasons). Note that GBSW actually
supports image (see example below). Also note that cton=ctof. This
is because the switiching is already included in GBSW.
NBOND atom switch cdie vdw vswitch -
ctonnb 16.0 ctofnb 16.0 cutnb 20.0
- Setup the input radii: the intrinsic atomic radii define the
location of the solute-solvent boundary and are one of the most
important phyiscal parameters for GBSW (and any GB/PB models
that allow radii input).
The file "radiius_gbsw.str" contains a set of input radii that have
been optimized for GBSW peptide simualtion (Nina et al, 1997; Chen et
al, JACS 2006). Note that this radii set should always be used
together with the GBSW-specific CMAP for best accuracy in peptide
- "Solvate" using GBSW: invoking GB solvent such as GBSW is very simple
gbsw sgamma 0.005 nang 50
"sgamma" is the effective surface tension coefficient (0.005 is
recommended for all GBSW simulations). "nang" is the number of angular
integration points. Larger nang increases the accuracy, but the
calculation becomes more expensive. nange=50 is necessary (and mostly
Once GBSW is setup, the rest is same as any "regular"
simulations, except for a few small differences. For example, there
is no pressure control (most GB models including GBSW are
parameterized to mimic 1 atm pressure and this is not adjustable)
and PME is not applicable. Either Nose-Hoover thermostat or Langevin
dynamics is typically used for temperature control.
2. GBSW implicit membrane simulation of phospholamban
This input illustrates a typical setup for simulations in GBSW
membrane without images. In this example, we will
- The raw PDB file needs to pre-processed by MMTSB/convpdb.pl (or
by another tool), mainly to extract the desired chain and/or model
and to add "segid" column.
convpdb.pl -chain A -model 1 1ZLL.pdb >! 1zll_monomer.pdb
convpdb.pl -model 1 -segnames 1ZLL.pdb >! 1zll_model1.pdb
- Generate the PSF for the pentameric channel (5X repeat operations
fro each chain) and read the initial coordinates. Many atoms
(mostly hydrogens) will still miss coordinates after
reading, mainly due to atom naming differences. CHARMM has built-in
facilities to build missing coordinates from known coordinates based
on the covalent geometry (defined either in IC tables or in parameter
- Orient the TM domains along Z and adjust their position in the
membrane (such that the C-terminal locates at the membrane
coor rotate ydir 1.0 phi 90.0
coor trans zdir -?zmin
coor trans zdir -17.0
- Set up input radii and nonbond options (see above)
- Request GBSW implicit membrane:
gbsw sgamma 0.005 nang 50 tmemb 30.0 msw 2.5
Compared to GBSW implicit solvent, the new keyword "tmemb"
activates the implicit membrane option of GBSW module. "msw" is the
half of switching length over which hydrophobic environment is
changed to solvent region. Thus, "tmemb-msw*2" is the hydrophobic
thichness of the membrane (25 A with the above).
- Minimize, equilibrate and run a very short production. You are
welcome to apply your (newly acquired) VMD and CHARMM analysis
skills to examine the results.
3. GBSW implicit membrane simulation with images
This input illustrates how to use GBSW membrane with images. We
will attempt to simulate the same system as in "gbswmemb1.inp". Only
one monomer is present, but a 5-fold sysmmetry is imposed to
describe the pentermic channel:
* 5-fold symmetry
ROTATE 0.0 0.0 1.0 72.0
ROTATE 0.0 0.0 1.0 144.0
ROTATE 0.0 0.0 1.0 216.0
ROTATE 0.0 0.0 1.0 288.0
The images must be set up before invoking GBSW. GBSW is
compatable with any kinds of images in solvent or membrane. The rest
of the script is exactly the same as "gbswmemb1.inp".