On 8/29/13 8:44 AM, Valentina wrote:
I have a layered double hydroxide structure: i.e a sheet with Metals (Al &
Mg), that are balanced by OH groups on both sides.
The sheet should be periodic in xy-direction and there are bonds between Al
and OH.
For this, obv., I am using in-house FF, that I assign with pdb2gmx.
In the molecule.rtp I specify bonds (Al-O, O-H) and angles (Al-O-H). There
are no dihedrals, hence nrexcl is set to 2. I also have LJ and Coulomb.
I run energy minimisation on a small cell containing 2 layers of mineral (
1.25680 x 1.08842 x 3.20000 + angles) and get an error on 32nd step.
May be cell is too small?
Possibly. What are your cutoffs? I would imagine that unit cell violates the
minimum image convention for all but the smallest cutoffs. I don't know what
your custom force field requires, though.
First, make your life easy. Run with a single layer to make sure that's stable
before adding a second layer.
-Justin
When I run without periodic_molecule = yes I do not have such issue.
Any help will be great!
Step= 31, Dmax= 9.9e-02 nm, Epot= 1.95744e+08 Fmax= 3.13311e+06, atom= 64
step 32: Water molecule starting at atom 404 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step= 32, Dmax= 1.2e-01 nm, Epot= 1.95737e+08 Fmax= 8.74156e+05, atom=
404
Step= 33, Dmax= 1.4e-01 nm, Epot= 1.95706e+08 Fmax= 2.39047e+05, atom= 50
A list of missing interactions:
Bond of 112 missing 4
Angle of 168 missing 18
exclusions of 535 missing 8
-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: domdec_top.c, line: 173
Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"They Were So Quiet About It" (Pixies)
--
View this message in context:
http://gromacs.5086.x6.nabble.com/periodic-molecule-missing-interactions-tp5010815.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* 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 gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
