[gmx-users] Re: simulation crash with GROMOS96 force field

[Vitaly V. Chaban]

Justin,

All the directives are correct. Chris just mistyped saying
>>> [ molecules ]
>>> CIP 3

instead of

[ moleculetype ]
CIP           3
that I orginally send him.

He can't know how many CIPs I have in my system because I didn't send
him this section. :)


Vitaly



On Sun, Jan 24, 2010 at 8:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Vitaly V. Chaban wrote:
>>>
>>> There's your problem (although in a different manner than I thought).
>>> If you have, for example, 3 solutes, then you should have
>>>
>>> [ molecules ]
>>> CIP 3
>>>
>>> -NOT-
>>>
>>> [ molecules ]
>>> CIP 1
>>
>> Of course, the number of moleules in .top and .gro files coincides.
>> Otherwise, one would have had immediate crash.
>>  CIP     3  -> [ moleculetype ] !
>>
>
> [molecules] is a different directive than [moleculetype].  Under
> [moleculetype] you find the name of the molecule and the number of
> exclusions, not the number of molecules.  Do you have only one solute?  If
> so, then it cannot be the first molecule in the system, given the atom
> numbers in the crash you reported before.  Is everything in the [molecules]
> directive in the same order as your coordinate file?  Did grompp give any
> atom type mismatch warnings?
>
> -Justin
>