[gmx-users] Re: Atoms are fused after inserting in membrane

[Dr. Vitaly Chaban]

> Does that mean the atoms will shrink and adjust at the time inflategro step
> and
> this closely packed lipids will stay apart? Because as you said the energy
> of course will be high on selected atoms during first EM step.
> Could you suggest me that, can I proceed as such with my system, since there
> is no problem in grompp and EM step (except high energy on some atom).


The energy will normalize during molecular dynamics stage.


Dr. Vitaly Chaban





> or Do I need to manually remove those overlapping lipids and water
> molecules.
>
> Thanks in advance
>