Dear Justin, you are definitely true. I tested with Gromacs 4.0.7 a couple of other proteins that were correctly minimized with the same machine and the previous version of Gromacs, and both of them stopped with the neighborsearching error. Then, I found a way to switch to version 4.0.5 on the same machine, and I minimized pretty well my model... Now the big difficulty will be saying to the administrators of the system that hosts my simulations that their installation is faulty...and I fear you will not able to help me...;-)
Thank you so much for all your invaluable help and time you spent on my problem. I also want to thank Luca Mollica for his precious support during these days. Best regards Anna -----Messaggio originale----- Da: Justin A. Lemkul [mailto:[email protected]] Inviato: martedì 25 maggio 2010 15.28 A: Anna Marabotti Oggetto: Re: R: coordinates and topologies of file "stepsize too small" Hi Anna, I strongly suspect the installation is faulty. I see no other explanation. Setting a box is easy: "editconf -c -bt dodecahedron." It may appear "strange" because most visualization software defaults to a triclinic rendering, but you can use "trjconv -pbc mol -ur compact" to get the correct box appearance. In the case of 1WBE, I used ~2000 fewer water molecules than your original system. -Justin Anna Marabotti wrote: > Dear Justin, > this is probably the key of my problem! GROMACS 4.0.7 has been just > installed on the machine I'm currently using, and this is my first > calculation using it (before, I was using version 4.0.5.). I'm not able to > answer to your question about compilers because I'm only a user of that > machine, but now I will try to repeat calculations using some systems that I > successfully used with version 4.0.5, and will see what happens, and if the > problem will repeat, I will contact the sysadmin to check with him the > installation! > Thank you very much for your help, I will keep gmx-users updated with the > (hopefully!) end of this story! > > Let me ask you just a further little question: do you use some particular > parameters when you solvate the system in a non-cubic box? I tried sometimes > in the past to use the dodecahedral box, but I obtained "strange" results, > and therefore I preferred to switch to the cubic one, although there are > much more water molecules to manage. Have you got some suggestions? > > Many thanks again and best regards > Anna > > -----Messaggio originale----- > Da: Justin A. Lemkul [mailto:[email protected]] > Inviato: martedì 25 maggio 2010 14.55 > A: Anna Marabotti > Oggetto: Re: coordinates and topologies of file "stepsize too small" > > > Hi Anna, > > I must admit I'm stumped. I was able to minimize the 1WBE structure just > fine, > both in vacuo (in a 10-nm cubic box) and in solution with a counterion > (dodecahedral solvent box, 1.0-nm solute-box distance). Both procedures > proceeded without problems, so I doubt that anything is wrong with your > template > structure. > > What compilers did you use to build Gromacs? Sometimes weird results happen > > from buggy compilers, but aside from your Gromacs installation being > nonfunctional, I don't know what's going on. Have you successfully worked > with > other systems with this particular Gromacs installation? > > -Justin > -- gmx-users mailing list [email protected] http://lists.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
