Alright, I understand now.
Many thanks for this!
Antoine
Le 29/08/2012 18:57, Mark Abraham a écrit :
On 30/08/2012 3:18 AM, Delmotte, Antoine wrote:
Many thanks for your quick response, Mark.
So epsilon_r is actually different from the actual relative
permittivity (which would be like 80 for water), is that right?
You can have an atomistic solvent or a continuum solvent, but not both
at once.
If so, how does one usually chooses this value of epsilon_r? Is the
default value of 1 applicable for most cases (like for simulations in
water), or should one obtain it from the literature somehow?
The force field defines it (normally to 1).
Mark
Thank you,
Antoine
On 29/08/12 14:47, Mark Abraham wrote:
On 08/29/2012 11:08 PM, Delmotte, Antoine wrote:
Dear Gromacs users,
I would like to know which charges are used by Gromacs in the
calculation of electrostatic interactions in the standard coulomb
potential:
E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12);
Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of
the force field used?
If you use pdb2gmx to generate your .top, yes. More generally,
GROMACS uses the charges found in the .top.
Could you also please redirect me towards the relevant literature
for the calculation of epsilon_r in Gromacs? (or does Gromacs uses
a fixed epsilon_r?)
You choose it. See parts of manual 4.1 and 7.3
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
