[gmx-users] Problems with solvation in SW (water shell model)
fileti at gmail.com
Mon Jul 9 18:14:30 CEST 2012
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
Syntax error - File sw.itp, line 36
Last line read:
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 ]
Done it, I got pre-process the files, but mdrun gave me the segmentation fault:
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?
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
Tel.: (12) 3309-9573
More information about the gromacs.org_gmx-users