[gmx-users] �ظ�: �ظ�: Re: Implicit Solvent and Box Size

[John Whittaker]

Hi,

As Justin mentioned, with implicit solvent, there is no "box". The solute
is simply diffusing through space. The idea of a simulation box is only
relevant when you are using PBC.

Despite having box vectors present at the bottom of your .gro file, these
don't really have a meaning if you're not using PBC. Similarly, if you
visualize the box using VMD, you will see it, but again it doesn't have a
physical meaning in the simulation.

With regards to your previous email: you mentioned that the molecules
"flew" out of the box. Did it seem as though the molecule was slowly
diffusing through space or did it seem like your system was exploding?

- John


> Dear Justin,
>
> I made the box with 'gmx ediconf'. Should I add some constraints for the
> box boundary for non-pbc box? Would you please give more hints? Thank you
> very much!
>
>
> Regards,
> Zhuo
>
> ________________________________
> ������: �� ׿ <zhangzhuo10 at hotmail.com>
> ����ʱ��: 2019��10��8�� 10:40
> �ռ���: gromacs.org_gmx-users at maillist.sys.kth.se
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> ����: �ظ�: Re: [gmx-users] Implicit Solvent and Box Size
>
> Dear Justin,
>
> I have tried implicit solvent without pbc or barostat. The box was not
> compressed but the molecules flew out of the box. I believe that it was
> because of nopbc box. Would you please give more information on why
> implicit solvent is used without pbc?
>
> Thanks��
>
>
> Regards,
> Zhuo
> --
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