[gmx-users] initial configuration problems and energy minimization

[Arun kumar]

Hi Mark.....
               Thanks for your suggestions.... I will use your
suggestions to solve the problem. And  then I will reply here about
the outcomes.....

Regards
Arun

On 5/18/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Arun kumar wrote:
> > Dear gmx-users,
> >                        Here I have a some problem regarding initial
> > configuration....  My system is composed of  cationic surfactants,
> > co-surfactants, water. I am able to minimize the energy of my
> > system(random), if it contains 15(surfactants)+ 15(co-surf)+
> > 1000(water)+
> > 15 (counterions) and also am able to simulate.......
> >
> >                       But when I increase the number of surfactants
> > or co-surfactants..... Even the energy of the system initially is a
> > big negative..... When I start true simulation, Potential energy is
> > becoming positive...and ultimately box is exploding [xtc error or some
> > times ci error]...... still I tried to minimize the energy of initial
> > configuration, but I am getting the same error.
> >
> > Below I describe the steps i took to do simulations
> >
> > 1)minimize the energy of surfactnat(btm.gro)(includes counterion) and
> > co-surfactant(str.gro) in Vaccum
> >
> > 2)Generate a system of 100 surfactnats(includes counterions), 20
> > co-surfactants and 1000 waters by using  packmol(random)
> >
> > 3)Minimize the whole system until potential will become a reasonable
> > negaive
> >
> > 4)With that minimized structure I run simulation but always the box is
> > exploding
> >
> > My simulation is successful when  the no of surf and co-surf are 15+15
> >
> > For this successful simulation Initially i am conducting a NVT
> > simulation with 0.01 fs timestep  at 100K temp and then another NVT at
> > desired temp(300K) and then NPT with 2fs timestep
>
> This looks pretty reasonable. You should check visually that packmol is
> not generating a conformation with atoms that are too close together.
> You can try using position restraints during your equilibration steps,
> and equilibrating for longer. The explosion is almost certainly
> happening because atoms are too close at some point, and these leads to
> huge energies. If your density is wrong for your NVT, then relaxing to
> NpT too quickly can cause this sort of problem too - use a large tau_t,
> or generate a box closer to the right size initially.
>
> Mark
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-- 
Arun kumar.V
M.E Chemical