[gmx-users] LINCS warnings and ligand topology

[MPI]

Hi Justin,

Thanks for your suggestions.
>Hacking off atoms because the simulation fails is a pretty bad strategy :)

Indeed, I removed all O atoms and S atom.  Simulations in solvent are
perfectly fine. This might suggest  that  the errors (warnings) came
directly from these deleted atoms, especially O3 indexed 2073.
131DRG     O3 2073   1.789   5.047   4.061

>It could also be a problem with your protocol and/or .mdp files, but only by
>systematically investigating what's going on will you figure out what the
>problem is.

The input mdp files are from your protein-lignad (JZ4) tutorial and
they work well with various (many other) ligands in other proteins
(systems in solvent) . However, this O3 atom 2073 with H  causes LINCS
warnings.

Also, I  tried  EM  for this ligand in vacuum and MD production in
vacuum.  It turns out  the system  of this ligand  only   is NOT
stable because of warnings as below.  It usually  dose not happen in
other ligands like JZ4.


############################
WARNING: Listed nonbonded interaction between particles 6 and 50
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

############################

Again,  is there a way to fix this ligand topology generated by prodrg
/Acpype because both methods have the same/similar output ?   The mdp
files in vacuum are attached.


Thanks,

Dewey



#em.mdp   in vaccum

cpp                      = /usr/bin/cpp
define                   = -DFLEXIBLE
integrator               = steep
nsteps                   = 5000
constraints              = none
emtol                    = 100.0
emstep                   = 0.01
nstcomm                  = 1
ns_type                  = simple
nstlist                  = 0
rlist                    = 0
rcoulomb                 = 0
rvdw                     = 0
Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
nstxout                  = 1
pbc                      = no

# md.mdp  in vacuum

cpp                      = /usr/bin/cpp
define                   = ;-DFLEXIBLE
integrator               = md
nsteps                   = 50000
constraints              = none
emtol                    = 100.0
emstep                   = 0.01
comm_mode                = angular
ns_type                  = simple
nstlist                  = 0
rlist                    = 0
rcoulomb                 = 0
rvdw                     = 0
Tcoupl                   = no
Pcoupl                   = no
gen_vel                  = no
nstxout                  = 1
pbc                      = no