[gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)
tsjerkw at gmail.com
Fri May 4 13:19:30 CEST 2007
You have to get your methods straight.., and be more clear in the
phrasing of your question.
> I am trying to simulate a surfactant-water
> system(also contains some co-surfactants). Surfactant is a cationic
> surfactant with chloride as counterion. And the cosurfactant is fatty
> alcohol. water is of spc model. I got topologies from Prodrg for my
> surfactant and cosurfactant.
What force field do you use? The standard output from PRODRG for
gromacs is the gmx force field, which is deprecated and shouldn't be
used (this is in the archives).
> So I minimized the energies for both my
> molecules. And prepared a system of 1400 waters, 20 surfactants, 20 counter
> ions and 40 cosurfactants in a box of 5X5X8 nm^3 using packmol.
Maybe you're better of trying one surfactant molecule and one chloride
in water to start with?
> I tried to minimize the energy of the system using
> l-bfgs. But I am always getting the error attached below. In my em.mdp file
> I am using pme for coulomb type. Even for MDRUN also I am getting the same
> error... I checked the previous posts and I am unable to understand what's
> the problem. And can anyone tell what is meant by broken topology??? Also
> try to help me to get out of the problem.
Even for MDRUN? pfff, that must be really bad then. First of all, do
you mean running the program 'mdrun' with the .tpr file for l-bfgs EM,
or an actual MD run? In case of the latter, wouldn't you think there's
little point in starting an MD run if energy minimization already
failed? In case of the former, the statement is redundant (now it's
> F-max = inf on atom 97
> F-Norm = nan
So, your system is exploding... Do you have any overlapping
bonds/atoms? Does your box actually contain your system? (Do think
periodically..., overlapping periodic images?).
> My topology contains a system of four types surfactant, cosurfctant, water
> and Chloride ions. Until grompp everything is fine. Total charge on system
> is zero. I can give any more details if it is needed.
Good, until grompp everything's fine. Now, then the error comes as a
surprise! But what did you do before? What steps did you take?
Oh, and I bet that in your .mdp file it says "tc-grps = SOL SUR ALC
CL", albeit that the actual names and the order of them may be
different. This is an issue, which has also been dealt with
extensively (including the past week). In any case, when reporting
that you've ran into a problem, it may be helpful to us to send your
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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