Re: [gmx-users] g_dipoles
On 2014-05-11 02:18, Nilesh Dhumal wrote:
I run g_dipoles for two ionic liquids : 1-Ethyl-3-methylimidazolium
chloride and 1-Ethyl-3-methylimidazolium ethylsulfate. In both the systems
cation is common 1-Ethyl-3-methylimidazolium.
I didn't follow the discussion but you can not use dipole moment
fluctuations to compute the dielectric constant for ionic species as
every ion that moves to the other side of the periodic box will increase
the fluctuations artificially.
In g_dipoles comde
static void neutralize_mols(int n,int *index,t_block *mols,t_atom *atom)
{
double mtot,qtot;
int ncharged,m,a0,a1,a;
ncharged = 0;
for(m=0; mn; m++) {
a0 = mols-index[index[m]];
a1 = mols-index[index[m]+1];
mtot = 0;
qtot = 0;
for(a=a0; aa1; a++) {
mtot += atom[a].m;
qtot += atom[a].q;
}
/* This check is only for the count print */
if (fabs(qtot) 0.01)
ncharged++;
if (mtot 0)
/* Remove the net charge at the center of mass */
for(a=a0; aa1; a++)
atom[a].q -= qtot*atom[a].m/mtot;
}
}
if (ncharged)
printf(There are %d charged molecules in the selection,\n
will subtract their charge at their center of
mass\n,ncharged);
}
For 1-Ethyl-3-methylimidazolium chloride, program don't print There are
%d charged molecules in the selection will subtract their charge at their
center ofand for other ionic liquids it do.
For 1-Ethyl-3-methylimidazolium ethylsulfate ionic liquid program show the
comment and recalculate the charges.
/* Remove the net charge at the center of mass */
for(a=a0; aa1; a++)
atom[a].q -= qtot*atom[a].m/mtot;
}
I don't know why program is not using same protocol for all system.
What could be the reason to remove the net charge at the center of mass
for dipole moment calculation.
Nilesh
On 4/27/14, 4:33 PM, Nilesh Dhumal wrote:
On 4/27/14, 4:25 PM, Nilesh Dhumal wrote:
On 4/27/14, 4:01 PM, Nilesh Dhumal wrote:
Hello,
I run g_dipoles for two different systems (System are ionic
liquids).
For one system when I run g_dipoles I get following message
There are 256 molecules in the selection
There are 256 charged molecules in the selection,
will subtract their charge at their center of mass
and I don't get this message for other system.
Why program subtract their charge at their center of mass for one
system
and not for other.
Based on whatever the topology says, g_dipoles doesn't find a net
charge
on
whatever these molecules are. Without providing more information -
what
the
molecules/selections are, what the topology(ies) is(are) - that's all
that
can
be surmised at this point.
-Justin
There are 128 cations (EMI) and 128 anions (ETS). Total charge is ZERO
here is molecular section from topology file.
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
#include emi.itp
#include ets.itp
[ molecules ]
; Compound#mols
EMI128
ETS128
For other system I have different anion. I didn't specify the number of
residues in molecular section.
[ system ]
; Name
Grunge ROck MAChoS t= 2.0
[ molecules ]
; Compound#mols
Ion 1
So Ion is some collection of molecules, or what? If it's a single
[moleculetype] composed of multiple molecules, each bearing a net charge
but
adding up to zero for the whole [moleculetype], this explains your
observation.
g_dipoles reads Ion as being a neutral entity, which is probably not
correct
for a program like g_dipoles.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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Dept. of Cell Molec. Biol., Uppsala University.
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Re: [gmx-users] g_dipoles
On 2014-05-11 15:31, Nilesh Dhumal wrote:
On 2014-05-11 02:18, Nilesh Dhumal wrote:
I run g_dipoles for two ionic liquids : 1-Ethyl-3-methylimidazolium
chloride and 1-Ethyl-3-methylimidazolium ethylsulfate. In both the
systems
cation is common 1-Ethyl-3-methylimidazolium.
I didn't follow the discussion but you can not use dipole moment
fluctuations to compute the dielectric constant for ionic species as
every ion that moves to the other side of the periodic box will increase
the fluctuations artificially.
I am not calculating the dielectric constant for my system. I am
calculating the dipole moment of the system. For dipole moment calculating
program put the periodic boundary condition off. I calculated the dipole
moment for two different systems. In one system program calculate the
total charge on residue and change is 1. Program will subtract their
charge at their center of mass for one system and for other system it
don't do. Both the system have cation and anion. Why program is not
following same protocol for both systems? Why program is subtracting atom
charges at their center of mass for dipole moment calculation.
Not sure why the program does what it does, but the total dipole of a
periodic system is not a meaningful quantity either. If you have a
cluster in vacuum it could make sense, but then the charges should not
be corrected.
Nilesh
In g_dipoles comde
static void neutralize_mols(int n,int *index,t_block *mols,t_atom *atom)
{
double mtot,qtot;
int ncharged,m,a0,a1,a;
ncharged = 0;
for(m=0; mn; m++) {
a0 = mols-index[index[m]];
a1 = mols-index[index[m]+1];
mtot = 0;
qtot = 0;
for(a=a0; aa1; a++) {
mtot += atom[a].m;
qtot += atom[a].q;
}
/* This check is only for the count print */
if (fabs(qtot) 0.01)
ncharged++;
if (mtot 0)
/* Remove the net charge at the center of mass */
for(a=a0; aa1; a++)
atom[a].q -= qtot*atom[a].m/mtot;
}
}
if (ncharged)
printf(There are %d charged molecules in the selection,\n
will subtract their charge at their center of
mass\n,ncharged);
}
For 1-Ethyl-3-methylimidazolium chloride, program don't print There are
%d charged molecules in the selection will subtract their charge at
their
center ofand for other ionic liquids it do.
For 1-Ethyl-3-methylimidazolium ethylsulfate ionic liquid program show
the
comment and recalculate the charges.
/* Remove the net charge at the center of mass */
for(a=a0; aa1; a++)
atom[a].q -= qtot*atom[a].m/mtot;
}
I don't know why program is not using same protocol for all system.
What could be the reason to remove the net charge at the center of mass
for dipole moment calculation.
Nilesh
On 4/27/14, 4:33 PM, Nilesh Dhumal wrote:
On 4/27/14, 4:25 PM, Nilesh Dhumal wrote:
On 4/27/14, 4:01 PM, Nilesh Dhumal wrote:
Hello,
I run g_dipoles for two different systems (System are ionic
liquids).
For one system when I run g_dipoles I get following message
There are 256 molecules in the selection
There are 256 charged molecules in the selection,
will subtract their charge at their center of mass
and I don't get this message for other system.
Why program subtract their charge at their center of mass for one
system
and not for other.
Based on whatever the topology says, g_dipoles doesn't find a net
charge
on
whatever these molecules are. Without providing more information -
what
the
molecules/selections are, what the topology(ies) is(are) - that's
all
that
can
be surmised at this point.
-Justin
There are 128 cations (EMI) and 128 anions (ETS). Total charge is
ZERO
here is molecular section from topology file.
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
#include emi.itp
#include ets.itp
[ molecules ]
; Compound#mols
EMI128
ETS128
For other system I have different anion. I didn't specify the number
of
residues in molecular section.
[ system ]
; Name
Grunge ROck MAChoS t= 2.0
[ molecules ]
; Compound#mols
Ion 1
So Ion is some collection of molecules, or what? If it's a single
[moleculetype] composed of multiple molecules, each bearing a net
charge
but
adding up to zero for the whole [moleculetype], this explains your
observation.
g_dipoles reads Ion as being a neutral entity, which is probably
not
correct
for a program like g_dipoles.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
[gmx-users] g_dipoles
Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Nilesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_dipoles
On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Based on whatever the topology says, g_dipoles doesn't find a net charge on whatever these molecules are. Without providing more information - what the molecules/selections are, what the topology(ies) is(are) - that's all that can be surmised at this point. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_dipoles
On 4/27/14, 4:25 PM, Nilesh Dhumal wrote: On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Based on whatever the topology says, g_dipoles doesn't find a net charge on whatever these molecules are. Without providing more information - what the molecules/selections are, what the topology(ies) is(are) - that's all that can be surmised at this point. -Justin There are 128 cations (EMI) and 128 anions (ETS). Total charge is ZERO here is molecular section from topology file. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include emi.itp #include ets.itp [ molecules ] ; Compound#mols EMI128 ETS128 You said you had two different systems. What's the difference between them? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_dipoles
On 4/27/14, 4:25 PM, Nilesh Dhumal wrote: On 4/27/14, 4:01 PM, Nilesh Dhumal wrote: Hello, I run g_dipoles for two different systems (System are ionic liquids). For one system when I run g_dipoles I get following message There are 256 molecules in the selection There are 256 charged molecules in the selection, will subtract their charge at their center of mass and I don't get this message for other system. Why program subtract their charge at their center of mass for one system and not for other. Based on whatever the topology says, g_dipoles doesn't find a net charge on whatever these molecules are. Without providing more information - what the molecules/selections are, what the topology(ies) is(are) - that's all that can be surmised at this point. -Justin There are 128 cations (EMI) and 128 anions (ETS). Total charge is ZERO here is molecular section from topology file. [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include emi.itp #include ets.itp [ molecules ] ; Compound#mols EMI128 ETS128 For other system I have different anion. I didn't specify the number of residues in molecular section. [ system ] ; Name Grunge ROck MAChoS t= 2.0 [ molecules ] ; Compound#mols Ion 1 Nilesh You said you had two different systems. What's the difference between them? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
