[gmx-users] initial configuration problems and energy minimization

Arun kumar arun.target at gmail.com
Fri May 18 00:21:00 CEST 2007

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)+
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

I don't know why I am unable to conduct with more no. of surfactants
in water..... I tried the samething for a bilayer initial
configuration also(generated by packmol), but getting same error....
Is there any solution to solve this??? I already checked archive lot
of times but i am unable to find anything relevant.................

I think its not that much related to gromacs...... But i need help to
solve this problem.... I can give any more details if it is

Thanks in advance
Arun kumar.V
M.E Chemical, IISc

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