Hi Arun,
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
just confusing).
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
.mdp file.
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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