Hello, I'm trying to solvate an OPLSAA methanol molecule in polarizable water shell. Initially I generated a box of pure water using the TIP5P box available in gromacs 4.5. I simulated pure water and I got all the bulk properties in agreement with published results for SW water. In sequence, I used genbox to add the SW water in a 3x3x3 box with a molecule of methanol. By using grompp I received the following error message when I tried minimization
Fatal error: Syntax error - File sw.itp, line 36 Last line read: 'LJ Geometric' Found a second defaults directive. Following a suggestion I found on the gmx-forum I commented the following lines of the sw.itp file. [ defaults ] LJ Geometric Done it, I got pre-process the files, but mdrun gave me the segmentation fault: Steepest Descents: Tolerance (Fmax) = 1.00000e+00 Number of steps = 5000 Segmentation fault: 11-02 nm, Epot= nan Fmax= 1.61425e+04, atom= 2380 Besides I can not minimize the solution, I also noticed that after I have commented the lines of the file sw.itp, I did not get back to simulate the pure water again. Anyone have any tips on how I could solve this problem? Bests eef _______________________________________ Eudes Eterno Fileti Instituto de Ciência e Tecnologia da UNIFESP Rua Talim, 330, São José dos Campos - SP Tel.: (12) 3309-9573 Página: sites.google.com/site/fileti/ -- 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
