I’ve a dual resolution system containing CG (Coarse Grained) and AA (All Atom) particles and using the hybrid pair style lj_sf_dipole_sf and lj_charmm_coul_charmm. According to a recent extension of the rRESPA integrator ( J. Chem. Theory Comput., 2015, 11 (10), pp 4749–4759 ) it is possible update at the outer rRESPA level all forces obtained by CG-CG interaction and update in the inner level CG-AA , AA-AA and bonded forces. How Is it possible separate rRESPA computations by specific pair interaction?
I’ve a dual resolution system containing CG (Coarse Grained) and AA (All Atom) particles and using the hybrid pair style lj_sf_dipole_sf and lj_charmm_coul_charmm. According to a recent extension of the rRESPA integrator ( J. Chem. Theory Comput., 2015, 11 (10), pp 4749–4759 ) it is possible update at the outer rRESPA level all forces obtained by CG-CG interaction and update in the inner level CG-AA , AA-AA and bonded forces. How Is it possible separate rRESPA computations by specific pair interaction?
Have a look at the documentation for pair style hybrid and run style research and let us know what exactly the step is, that you are struggling with.
My system comprises a explicit CHARMM protein inside a box containing ELBA-CG water molecules. The interaction between CG-ELBA water and the explicit atoms ( CG-AA interactions), as well as the auto-interaction between CG water beads (CG - CG interactions) is given by the pair style lj_sf_dipole_sf. The interaction between explicit - explicit atoms (AA-AA) is given by lj_charmm_coul_long.
I would like to update the CG-CG pair interactions (water-water) at the outer rRESPA level (~10ns), and update pair interactions between CG-AA at the inner level (at ~2ns), but I didn’t figure out how to use keyword ‘hybrid’ ‘pair’ or the ‘inner/middle/outer’ to specify CG-CG and CG-AA interactions in different levels of hierarchy, since the forces are obtained by the same pair style (lj_sf_dipole_sf) for both.
My system comprises a explicit CHARMM protein inside a box containing ELBA-CG water molecules. The interaction between CG-ELBA water and the explicit atoms ( CG-AA interactions), as well as the auto-interaction between CG water beads (CG - CG interactions) is given by the pair style lj_sf_dipole_sf. The interaction between explicit - explicit atoms (AA-AA) is given by lj_charmm_coul_long.
I would like to update the CG-CG pair interactions (water-water) at the outer rRESPA level (~10ns), and update pair interactions between CG-AA at the inner level (at ~2ns), but I didn’t figure out how to use keyword ‘hybrid’ ‘pair’ or the ‘inner/middle/outer’ to specify CG-CG and CG-AA interactions in different levels of hierarchy, since the forces are obtained by the same pair style (lj_sf_dipole_sf) for both.
Yes, but pair_style hybrid allows to specify the same pair_style twice.
My system comprises a explicit CHARMM protein inside a box containing
ELBA-CG water molecules. The interaction between CG-ELBA water and the
explicit atoms ( CG-AA interactions), as well as the auto-interaction
between CG water beads (CG - CG interactions) is given by the pair style
lj_sf_dipole_sf. The interaction between explicit - explicit atoms (AA-AA)
is given by lj_charmm_coul_long.
I would like to update the CG-CG pair interactions (water-water) at the
outer rRESPA level (~10ns), and update pair interactions between CG-AA at
the inner level (at ~2ns), but I didn't figure out how to use keyword
'hybrid' 'pair' or the 'inner/middle/outer' to specify CG-CG and CG-AA
interactions in different levels of hierarchy, since the forces are obtained
by the same pair style (lj_sf_dipole_sf) for both.
Yes, but pair_style hybrid allows to specify the same pair_style twice.
FYI, here is an example for using the hybrid respa method based on the
melt example.
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 2 box
create_atoms 1 box
mass 1 1.0
mass 2 1.0
region half block -0.1 4.9 0 10 0 10
set region half type 2
the following error occurs “ERROR: Compute ti pair style does not exist (…/compute_ti.cpp:139)”
When tested the same ti compute above, in the absence of duplicity, the calculation is performed normally. What is the correct way to invoke the compute ti when I define the same pair style twice?
the following error occurs "ERROR: Compute ti pair style does not exist
(../compute_ti.cpp:139)"
When tested the same ti compute above, in the absence of duplicity, the
calculation is performed normally. What is the correct way to invoke the
compute ti when I define the same pair style twice?
there isn't any (yet). check the documentation! does it say anywhere
how you specify this? all compute, fix and other styles that support
hybrid pair styles with multiple references to the same pair style
explicitly state in the documentation, how this has to be done.