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

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 24 19:49:17 CET 2010

Vitaly V. Chaban wrote:
> 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. :)

You said before:

"> > 5. What does your .top look like? (does it list the organic molecule
 > > only once in the [ molecules ] section?)

Only once."

Does this mean you have only one solute?  Or that you have only one entry for 
solute, which you then have multiple molecules of in the system?  There 
certainly can be confusion if you aren't describing your system clearly.

The reason for asking is that the problematic atom numbers (which are greater 
than 42, as Chris pointed out) would indicate one of two possibilities:

1. CIP is present multiple times, and one of those molecules (at least) is 
having a problem.
2. There is one CIP, it does not appear as the first molecule in the system (due 
to the numbering), and perhaps (as I suggested) there was some sort of incorrect 

If neither of these is true, then it is important to know.


> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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