[gmx-users] (no subject)

[nicolis@guideo.fr]

Sorry my mail server had problems so I post again.

Hello,
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 221.69p
s) the density, temperature, energies (KE, PE, LJ, Coulomb, dispersion, LR 
etc), volume, x,y,z, of the box seam stable oscillating aro
und reasonable values. Looking at the ngmx animation, everything looks fine 
as well. But then, after step 221690 I get a crash. Here i
s 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 fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the!
 x-axis an
d 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 ty
pes from explicit hydrogens to combined CH3 in the topology and in the =!
0D
coord
inates 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