Hai Tsjerk, David, Mark and others,
Thank you for all
your responses. I had been successful in setting up simulation and
also in understanding what David and Mark told. As Dr. David
suggested, I started EM for single surfactant in vaccum and successful
in minimizing the energy. Also I did EM for my co-surfactant stearyl
alcohol and had been successful. Then I started minimizing the energy
of a system of 500 waters+ 1 cationic surf+ 1 fatty alcohol. It also
worked fine. And I started true dynamics(MD) of the bulk system and
had been successful. I think all these posts will be useful for others
who start gromacs with these kind of systems. So for me, Now the only
problem is getting correct forcefield for my surfactant system to get
good physical properties. I will post the topology for my surf and
co-surf when I will be successful in doing that.
Thanks and Regards
Arun Kumar
On 5/6/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
Arun kumar wrote:
> Hi Tsjerk and others,
> I tried to simulate one surfactant and one
> chloride ion in 500 waters and got similar type of errors. I mean my
> system got collapsed for l-bfgs minimization and for steepest descent
> the potential energy is a large number.(obviously some bad contacts).
> It seems the problem is with topology. Earlier I asked about what is
> meant by broken topology?? Can anyone tell what may ne the problem and
> also about what is meant by broken topology??
A broken topology is where you haven't managed to describe the bond
connectivity in your .top file that you'd like to. The way to fix it is
to reduce your problem to its simplest form (single surfactant in
vacuum, as David suggests), observe where the breakage occurs, read
chapter 5 carefully, and remedy appropriately.
Mark
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Arun kumar.V
M.E Chemical
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