[gmx-users] set charge as 0 in gromacs code
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_amdatoms-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]);
mdatoms-chargeA[stone_a]=0.0;
break;
}
}
Thanks,
Stony
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RE: [gmx-users] set charge as 0 in gromacs code
Hello Mark,
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?
Stony
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Mark Abraham [mark.j.abra...@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?
Mark
On Wed, Aug 7, 2013 at 1:16 AM, Shi, Yu (shiy4) sh...@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_amdatoms-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]);
mdatoms-chargeA[stone_a]=0.0;
break;
}
}
Thanks,
Stony
--
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[gmx-users] how to set charge 0 in the source code for PME
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[gmx-users] Default Electrostatic Algorithm for User Defined Potential
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