[gmx-users] Problems with solvation in SW (water shell model)

Eudes Fileti 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

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?
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/

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