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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.