Leontyev Igor wrote:
I just switched from the version 3.3 to 4.0. It turned out that the
4.0
version does not allow to run a parallel simulation of my protein in
vacuum. The protein consists of 2 chains and 4 separated (no bonds
with
chains) co-factors. For vacuum simulation 'pbc=no' which makes to use
particle decomposition option "-pd" of mdrun. In this case the
automatic
particle distribution over the nodes leads to the error:
"Fatal error:
Shake block crossing node boundaries
constraint between atoms (11191,11193)"
In the previous version 3.3 I used manual balancing with the "-load"
option to avoid the problem. In the current version 4.0 I did not
find
anything similar for the particle decomposition. Is there a way to
run
parallel simulations of the protein in vacuum?
I'd suggest updating to 4.0.4 for the copious bug fixes, one of which
might solve your problem. I can't think of a good reason offhand why
PD
or DD should be necessary for non-PBC simulations in vacuo - try both.
If you've still got your problem, let us know.
Mark
Gromacs-4.0.4, which I use, does not allow DD in non-PBC simulations.
Only
PD options is available. But PD has no flexibility to manually
redistribute
particles over the nodes. As written in the manual "With PD only whole
molecules can be assigned to a processor". Does it mean that there is
no way
to start PD parallel simulations of whole protein? In other words, does
it
means that there is no way to run parallel simulation of protein in
vacuum?
You can do it the way all the other programs do: only use constraints on
bonds involving H, and reducing the timestep to 1 fs.
I try to run MD with only constrained h-bonds (constraints = hbonds)
which allow 2fs timestep. The timestep 1fs would be needed if there will
be vibrating (unconstrained) h-bonds. But you suggest to use constraints
or it was a misprint?
This is subject to discussion, see e.g. gromacs manual. Actually, with all
bonds constrained 2 fs is already a large time step, and with only bonds
containing H constrained 1 fs is also quite large. A further discussion
can be found in the P-Lincs paper IIRC (J. Chem. Theor. Comp. 4 (2008) p.
116).
Thank you for the reference. The subject is what I would like to know in
more details. Regarding the problem that "Shake block crossing node
boundaries", the "-load" option implemented in gromacs-3.3.3 seems to remain
the most computationally efficient due to the larger, at least technically,
2fs timestep.
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