[gmx-users] R: neighborsearching error

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 17 13:05:03 CET 2009

Anna Marabotti wrote:
> I'm resending the message without attachments, since the previous one was filtered because it was too big.
> Please let me know how to send infos without being filtered, if more information are needed to help me. I
> tried again and again, changing settings and options for minimization, but I had no results until now.
> Best regards
> Anna
> Dear all,
> I'd need some help to understand a problem. I'm preparing my system (a protein of 157 residues in a box of
> 7507 water molecules and 11 Na+ ions) for a MD. During energy minimization, the program saves some .pdb files
> claiming that it was not able to settle some water molecules, but the minimization finishes regularly
> producing a .pdb file, and the system converges to the required force in a number of steps lower than the
> nsteps set in the em.mdp file. When I'm launching the PR-MD, the simulation stops with the "neighborsearching
> error", and in the .log file there are alerts indicating that other water molecules cannot be settled. I
> checked the files and found no problems on the minimized .pdb file: I cannot see any bump or collision.
> However, to be sure, I removed the water molecules "not settled" as indicated in the .log file after
> minimization, and repeated the PR-MD: error again, and a lot of "stepXXX.pdb" molecules. 
> The potential energy of my system after minimization seems to be quite reasonable and the molecule seems to be
> minimized to convergence. I tried adding other minimization steps, but nothing changes. The same if I reduce
> the step. I inspected the protein, but I did not find anything anomalous on it; on the other hand, problems
> seem to arise from water molecules only, not from protein, so I assume that its coordinates are correct.
> However, when I'm inspecting the system, also water molecules appear to be correct. The only thing I notice is
> that the "anomalous" water molecules are at the boundary of the box.

Removing the "problematic" water molecules is not a solution; you should have 
found that in the list archive.  Often these water molecules are the victim of 
some larger perturbation in your system (i.e., other molecules going shooting 
off through the box).

If the problems are always at the boundary, is your box size appropriate?  Do 
you have voids where solvent should be, but is not?  Check out your system with 
ngmx to make sure that you have fully solvated your unit cell.


> Could you please suggest me how to manage this problem? I looked into the gmx-user list archive but found
> nothing that seems applicable to my case.
> I'm attaching here the .log files from minimization and PR-MD (after minimization and after minimization and
> water removal). Please let me know if you need some other infos.
> Many thanks and best regards.
> Anna
> ______________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Skype: annam1972
> E-mail: amarabotti at isa.cnr.it
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
> ____________________________________________________
> "If you think you are too small to make a difference, try sleeping with a mosquito"
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list