Igor Leontyev wrote:
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.
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[email protected] [email protected] http://folding.bmc.uu.se
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
