[gmx-users] Re: methanol box of gromacs

[nicolis@guideo.fr]

Last attempt to post from this webmail server, I hope you don't get four 
copies of the mail and that you get more than the first line. Sorry about that.

I reply with a copy to the list because I have problems equilibrating the box.
Actually, it "looks" equilibrated. I mean that I begin a 1ns simulation and for 
the first 221690 steps (1fs each, so the first 221.69ps) the density, 
temperature, energies (KE, PE, LJ, Coulomb, dispersion, LR etc), volume, x,y,z, 
of the box seam stable oscillating around reasonable values. Looking at the 
ngmx animation, everything looks fine as well. But then, after step 221690 I 
get a crash. Here is the output:

********************begin mdrun output**************
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the 
second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         NaN,          NaN,   !
       NaN
}
            Box[    1]={         NaN,          NaN,          NaN}
            Box[    2]={         NaN,          NaN,          NaN}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the 
second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         NaN,          NaN,          NaN}
            Box[    1]={         NaN,          NaN,          NaN}
            Box[    2]={         NaN,          NaN,          NaN}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the 
second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         NaN,          NaN,          NaN}
            Box[    1]={         NaN,          NaN,          NaN}
            Box[    2]={         NaN,          NaN,          NaN}
        !
 Can not f
ix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the 
second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         NaN,          NaN,          NaN}
            Box[    1]={         NaN,          NaN,          NaN}
            Box[    2]={         NaN,          NaN,          NaN}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the 
second vector in the xy-plane are supported.
         Box (3x3):
            Box[    0]={         NaN,          NaN,          NaN}
            Box[    1]={         NaN,          NaN,          NaN}
            Box[    2]={         NaN,          NaN,          NaN}
         Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the 
second vector in the xy-plane are supported.
         !
Box (3x3):

            Box[    0]={         NaN,          NaN,          NaN}
            Box[    1]={         NaN,          NaN,          NaN}
            Box[    2]={         NaN,          NaN,          NaN}
         Can not fix pbc.
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
********************end mdrun output**************
Of course I looked at the box size but at the last recorded step it is OK. Any
ideas, suggestions, help?

>        I read your writing on gromacs message list. I want to study a 
> small pharmaceutical molecule solvated in methanol by restrained MD 
> through Gromacs, so I'm wondering if I can use your equilibrated box of 
> methanol because you cited this box was generated from OPLS and I want 
> to use ffgmx or gromos96.

As for the use of an OPLS topology with ffgmx or gromos96, I don't think it's 
possible because you will have to change all !
the atom t
y
pes from explicit hydrogens to combined CH3 in the topology and in the 
coordinates and then reequilibrate. It would be simpler to use 
directly the $GMXDATA/top/methanol.itp topology included with the 
distribution and make a box of it.

>      
> cheers,
>  
> Songbai Liu

Anyway, as I had said before, when I resolve this NaN box vectors problem I 
will deposit the box in the gromacs site for whom t might 
want to use it.

Yiannnis