Protein_ligand simulation

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1

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I am performing an MD simulation of a protein-ligand complex. Minimization, heating and equilibration went smoothly. The production run was also completed but the .err file shows the following warning:

“WARNING 1 [file compl.top, line 79509]:
There are atoms at both ends of an angle, connected by constraints and
with masses that differ by more than a factor of 13. This means that
there are likely dynamic modes that are only very weakly coupled. To
ensure good equipartitioning, you need to either not use constraints on
all bonds (but, if possible, only on bonds involving hydrogens) or use
integrator = sd or decrease one or more tolerances:
verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=
4 or SHAKE tolerance <= 1e-05”
if I check that line in the compl.top file is the last one and it´s about chlorine ions.
I get this warning only if I run the simulation on one cluster (kebnekaise), while if I try to run on a different cluster (abisko), there is not warning at all.

here there are the settings for the simulation:

integrator = md

tinit = 0
dt = 0.002

nsteps = 50000000

simulation_part = 4

comm-mode = Linear

nstcomm = 100

comm-grps =

ld-seed = -1

nstxout = 100000
nstvout = 100000
nstfout = 0

nstlog = 10000
nstenergy = 2500

nstxtcout = 2500
xtc-precision = 1000

xtc-grps =

energygrps = Protein Other Water_and_ions

cutoff-scheme = Verlet

nstlist = 40

ns_type = grid

pbc = xyz
periodic_molecules = no

rlist = 1.4

coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 1.4

epsilon_r = 1
epsilon_rf = 1

vdw-type = Cut-off

rvdw = 1.4

DispCorr = No

table-extension = 10.0

fourierspacing = 0.12

pme_order = 4

implicit_solvent = No

gb_algorithm = Still

Tcoupl = v-rescale

nsttcouple = 5

tc-grps = Protein Other Water_and_ions

tau_t = 0.1 0.1 0.1
ref_t = 300 300 300

Pcoupl = Parrinello-Rahman
Pcoupltype = Isotropic
nstpcouple = 20

tau-p = 1
compressibility = 4.5e-5
ref-p = 1.0

refcoord_scaling = All

gen_vel = no

constraints = all-bonds

constraint_algorithm = lincs

continuation = yes

lincs-order = 4

lincs-iter = 1

lincs_warnangle = 90.0

morse = no

what does that warning mean?

Best,
Mary

2

What is defined on this line? Which atoms?

3

on that line you find chlorine ions to neutralize the complex

4

OK so it is a case in which grompp gets to the end of the topology and reports that there is a problem somewhere.

Which force field are you using? And which angle(s) may have super-heavy elements on one end? Is it correct to constrain all bonds? This is the origin of the problem.