Hello.
I am trying to simulate a multi-domain protein using the Martini
coarse-grained force field. The system consists of ~1600 protein "atoms"
and ~26000 Martini water "beads". The water box is large compared to the
size of the protein because of the significant conformational changes. The
protein has an elastic network with the following parameters: lower cutoff:
0.5 nm, upper cutoff: 0.9 nm, force constant: 500 kJ/(mol*nm). Elastic
"bonds" between atoms in two different domains were removed.

The MD parameters are similar to this:
http://cgmartini.nl/cgmartini/images/parameters/exampleMDP/martini_v2.x_new-rf.mdp

My first simulation was running on a supercomputer, 96 CPU cores. The
simulation crashed after ~2760000 steps:

A list of missing interactions:
       Harmonic Pot. of   2821 missing      1

Molecule type 'Protein'
the first 10 missing interactions, except for exclusions:
       Harmonic Pot. atoms 1098 1306           global  1098  1306
Fatal error:
1 of the 8124 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.317 nm) or the two-body cut-off distance (1.317 nm), see option -rdd,
for pairs and tabulated bonds also see option -ddcheck

Second simulation (-rdd was set to 1.6, 72 CPU cores) crashed after
~70170000 steps:

Fatal error:
The X-size of the box (9.696262) times the triclinic skew factor (0.990125)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.600000)

Third simulation (rdd=1.5, 48 CPU cores) crashed after 24939840 steps:

Step 24939840: The domain decomposition grid has shifted too much in the
Y-direction around cell 2 3 0 (2 3 2, 3 3 0, 1 3 1, 2 3 1, 3 3 1, 1 3 2, 3
3 2, 1 3 0, 0 3 0, 0 3 2, 0 3 1). This should not have happened. Running
with less nodes might avoid this issue. (12 error messages).

What MD/domain decomposition parameters should I use?

Thanks in advance.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to