On 7/20/12 6:46 AM, radhika jaswal wrote:
Dear all,
I did NVT simulations of a number of molecules with double bond. But when i
analysed the results i realised that double bond has been converted to single
bond and sp2 hybridisation has also changed to sp3. I was doing with all bonds
constraint option. But when i started with all angles constraint option it kept
on processing on version 3.3.1 and with many fatal errors on version 4.5.4.
Bonds do not break and form in classical MD, and hybridization cannot change.
If you are observing distortions in the structure, then likely your topology is
ill-suited to address the atoms involved. Correct use of improper dihedrals
should keep sp2 groups planar.
<snip>
-------------------------------------------------------
Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given
box and a minimum cell size of 1.69222 nm
Change the number of nodes or mdrun option -rcon or your LINCS settings
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Not all systems can be divided into any arbitrary number of DD cells. See here:
http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
