[gmx-users] set charge as 0 in gromacs code
Shi, Yu (shiy4)
shiy4 at mail.uc.edu
Wed Aug 7 03:28:10 CEST 2013
Thanks for your reply!!!
Not self energy term.
For my research reason, I would like to turn off the long-ranged electrostatics between
SOL and CL. That is to say, SOL and CL only interacts with erfc(eta*r)/r potential, without
reciprocal electrostatics parts.
I use PME in the mdp file for coulomb, and in topol file the CL is -1 charged.
Hence I have to set CL charge as 0 in the Gromacs code to turn off the reciprocal calculation of
the pme scheme. E.g before gmx_pme_do(), I set Cl charge as 0, but this fails to work.
So do you some idea to do this?
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [mark.j.abraham at gmail.com]
Sent: Tuesday, August 06, 2013 8:20 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] set charge as 0 in gromacs code
Ewald self energy, perhaps?
On Wed, Aug 7, 2013 at 1:16 AM, Shi, Yu (shiy4) <shiy4 at mail.uc.edu> wrote:
> Hello everyone,
> My system is 512 waters and 1 ion CL-. Now I would like to change the CL charge as 0 in the gromacs code for the short non-bonded interaction. While for the long-range electrostatics (pme) the CL is -1.
> My gromacs version is 4.6.2, which automatically starts 8 threads to compute.
> In src/kernel/md.c, at line 1191 just before function do_force() , I added codes as following which could find out which atom is CL and change its charge as 0 in a certain thread. After this, when I use g_energy, the Coul.SR of SOL and CL is -88 kJ, which should be 0 kJ.
> Does anyone could help me out?
> int stone_a;
> for (stone_a=mdatoms->start; stone_a<mdatoms->start+mdatoms->homenr; stone_a++)
> if (mdatoms->chargeA[stone_a] == -1.0)
> fprintf(stderr,"the atom %d found with charge %f\n", stone_a,mdatoms->chargeA[stone_a]);
> gmx-users mailing list gmx-users at gromacs.org
> * 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
gmx-users mailing list gmx-users at gromacs.org
* 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-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users