[gmx-users] Collision

[Dallas Warren]

This all sounds like
http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc

Remember, the box is just a visualisation of what the system looks like,
and you can move that box anywhere.  What is in the center of the box is
entirely up to you and the post processing you do.  What comes out of the
mdrun engine is arbitrary.

With VMD, and I suspect the other MD visualisation software such as pymol,
you can turn on the periodic images. Have you done that to see where things
are actually located?  What did you see?  Have you actually processed it
using trjconv to put it back in the center of the box to see what is
actually going on?  What command did you use, and how did it then look?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sat, 29 Feb 2020 at 09:15, Mohamed Abdelaal <m.b.abdelaal at gmail.com>
wrote:

> 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
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