[gmx-users] PME question, again

Ivano Eberini Ivano.Eberini at unimi.it
Wed Jun 19 09:09:44 CEST 2002

Dear Erik,
I run 1 ns molecular dynamics of a protein in water with PME. To obtain 
a neutral system, I put 8 Na ions in the box. One of them moved across 
the box boundary during dynamics. Should I rerun MD with a wider box? I 
usually try to minimize the box dimensions to reduce the computing time. 
Is there any way to evaluate the effect of this ion moving across the 
box upon the MD?

Thanks and best regards,


Mercoledì, giugno 19, 2002, alle 04:54 , Erik Lindahl ha scritto:

Hank deHaan wrote:

Thanks very much for your reply,
it helps to clarify the situation greatly

Any chance of elaborating on the strange effects
of charges moving across box boundaries?

Well, imagine you have a charge -1 in the center of the box, and +1 next 
to one of the box sides. This will give you a net dipole
in the system. Now, if the +1 charge moves across the box boundary and 
reappears on the other side the dipole will suddenly have
the opposite direction after a discrete instantaneous jump.

Ideally, you should use a box that is large enough so you don't have to 
consider effects on the scale of the box of course....



gmx-users mailing list
gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the www 
interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list