[gmx-users] R: neighborsearching error

Anna Marabotti anna.marabotti at isa.cnr.it
Tue Feb 17 12:52:44 CET 2009

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

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.

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 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"

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