[gmx-users] Collision

[Mohamed Abdelaal]

Hello all,

I created a graphene sheet and performed energy minimization, after energy
minimization I found that parts of the graphene sheet was moved from the
box bottom to the box topside at the same place (as if it was translated
upwards). I looked online for the problem and I understood that I should
restrain the graphene sheet along the z axis. I did that using force =1000.
and the problem was solved and nothing moved.

After that I tried to insert 25 molecule of (C60) inside a box which
contains the graphene sheet. I did that and did the energy minimization but
part of the  graphene sheet moved again from its place although the maximum
force was less than 1000 which is the force I used to restrain the graphene
sheet. However I didn't have any error during the energy minimization. Does
this means that the problem is just in visualization or I might have a
problem in my energy minimization ?

It is also worth mentioning that the C60 molecules are not spherical as it
should be. I read about that and I found people mentioning that this shape
deformation in only a visualization problem and can be solved by using gmx
trjconv. is it possible that this problem has happened to my whole system
including the graphene sheet or it shouldn't affect my graphene sheet as
long as I have restrained it ?

more info:
I used   periodic_molecules = yes while trying to minimize my whole system.
(I also tried without it but no impact)
I wrote:

gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p
C60_GRM_box.top -o min1.tpr -maxwarn 2

followed by
gmx mdrun -v -deffnm min1

and I got the below result:
writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 3293 steps
Potential Energy  =  6.3598562e+05
Maximum force     =  9.9486487e+02 on atom 12087
Norm of force     =  6.5454323e+01

Can anybody help me please.

Thanks

Mohamed