Re: [gmx-users] how to simulate a line charge
Justin, when i define the whole line charge as a charge group i do get a
coulomb energy contribution. I thought there would be no non-bonded
contribution. I use a very high cut-off (longer than chain length) and no
pbc. Am i missing something ?
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey kgp.a...@gmail.com wrote:
I was not sure if changing the size of maxcg would not negatively influence
anything else. I will give it a try. Thanks Justin
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then grompp worked fine but
the mdrun did not start. The following error came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 64
/* Verify whether largest charge group is = max cg.*
* This is determined by the type of the local exclusion type *
* Exclusions are stored in bits. (If the type is not large*
* enough, enlarge it, unsigned char - unsigned short - unsigned
long)*
*/
The solution is described in the comment above.
maxcg = sizeof(t_excl)*8;
Increase the size here.
-Justin
if (nr_in_cg maxcg)
{
gmx_fatal(FARGS,Max #atoms in a charge group: %d %d\n,
nr_in_cg,maxcg);
}
--
==**==
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==**==
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Re: [gmx-users] how to simulate a line charge
Amit Choubey wrote:
Justin, when i define the whole line charge as a charge group i do get a
coulomb energy contribution. I thought there would be no non-bonded
contribution. I use a very high cut-off (longer than chain length) and
no pbc. Am i missing something ?
Without seeing your .mdp file and the actual energy terms you're observing, I
can only guess. One would think that if it is the only molecule in the system,
there should be no intermolecular Coulombic terms (unless maybe some arise due
to periodicity, but in that case you do not have an infinite system and then
they are artifacts). There may be intramolecular terms (like 1-4) or
PME-related terms.
-Justin
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey kgp.a...@gmail.com
mailto:kgp.a...@gmail.com wrote:
I was not sure if changing the size of maxcg would not negatively
influence anything else. I will give it a try. Thanks Justin
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then grompp
worked fine but the mdrun did not start. The following error
came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 64
/* Verify whether largest charge group is = max cg.*
* This is determined by the type of the local exclusion
type *
* Exclusions are stored in bits. (If the type is not large*
* enough, enlarge it, unsigned char - unsigned short
- unsigned long)*
*/
The solution is described in the comment above.
maxcg = sizeof(t_excl)*8;
Increase the size here.
-Justin
if (nr_in_cg maxcg)
{
gmx_fatal(FARGS,Max #atoms in a charge group: %d
%d\n,
nr_in_cg,maxcg);
}
--
==__==
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==__==
--
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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Re: [gmx-users] how to simulate a line charge
Following is the mdp file
cpp = /usr/bin/cpp
;define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 1
;
; Energy minimizing stuff
;
emtol = 200
emstep = 0.01
pbc = no
nstcomm = 0
ns_type = grid
coulombtype = Cut-off
rlist = 60
rcoulomb= 60
rvdw= 60
Tcoupl = no
Pcoupl = no
gen_vel = no
E_x = 1 0 0
E_y = 1 0 0
E_z = 1 0 0
Following is the energy term
Step Time Lambda
00.00.0
Energies (kJ/mol)
Bond AngleLJ (SR) Coulomb (SR) Potential
1.11496e-070.0e+000.0e+009.90561e+059.90561e+05
Pressure (bar)
0.0e+00
Step Time Lambda
11.00.0
Energies (kJ/mol)
Bond AngleLJ (SR) Coulomb (SR) Potential
7.55922e-020.0e+000.0e+009.90324e+059.90324e+05
Pressure (bar)
0.0e+00
Amit
On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Justin, when i define the whole line charge as a charge group i do get a
coulomb energy contribution. I thought there would be no non-bonded
contribution. I use a very high cut-off (longer than chain length) and no
pbc. Am i missing something ?
Without seeing your .mdp file and the actual energy terms you're observing,
I can only guess. One would think that if it is the only molecule in the
system, there should be no intermolecular Coulombic terms (unless maybe some
arise due to periodicity, but in that case you do not have an infinite
system and then they are artifacts). There may be intramolecular terms
(like 1-4) or PME-related terms.
-Justin
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey kgp.a...@gmail.commailto:
kgp.a...@gmail.com wrote:
I was not sure if changing the size of maxcg would not negatively
influence anything else. I will give it a try. Thanks Justin
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then grompp
worked fine but the mdrun did not start. The following error
came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 64
/* Verify whether largest charge group is = max cg.*
* This is determined by the type of the local exclusion
type *
* Exclusions are stored in bits. (If the type is not
large*
* enough, enlarge it, unsigned char - unsigned short
- unsigned long)*
*/
The solution is described in the comment above.
maxcg = sizeof(t_excl)*8;
Increase the size here.
-Justin
if (nr_in_cg maxcg)
{
gmx_fatal(FARGS,Max #atoms in a charge group: %d
%d\n,
nr_in_cg,maxcg);
}
-- ==**__==
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==**__==
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Can't post? Read
Re: [gmx-users] how to simulate a line charge
Amit Choubey wrote:
Following is the mdp file
cpp = /usr/bin/cpp
;define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 1
;
; Energy minimizing stuff
;
emtol = 200
emstep = 0.01
pbc = no
nstcomm = 0
ns_type = grid
coulombtype = Cut-off
rlist = 60
rcoulomb= 60
rvdw= 60
Tcoupl = no
Pcoupl = no
gen_vel = no
E_x = 1 0 0
E_y = 1 0 0
E_z = 1 0 0
Following is the energy term
Step Time Lambda
00.00.0
Energies (kJ/mol)
Bond AngleLJ (SR) Coulomb (SR) Potential
1.11496e-070.0e+000.0e+009.90561e+059.90561e+05
Pressure (bar)
0.0e+00
Step Time Lambda
11.00.0
Energies (kJ/mol)
Bond AngleLJ (SR) Coulomb (SR) Potential
7.55922e-020.0e+000.0e+009.90324e+059.90324e+05
Pressure (bar)
0.0e+00
I suspect that energy terms comes from the use of an electric field, which you
had not mentioned before.
-Justin
Amit
On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Amit Choubey wrote:
Justin, when i define the whole line charge as a charge group i
do get a coulomb energy contribution. I thought there would be
no non-bonded contribution. I use a very high cut-off (longer
than chain length) and no pbc. Am i missing something ?
Without seeing your .mdp file and the actual energy terms you're
observing, I can only guess. One would think that if it is the only
molecule in the system, there should be no intermolecular Coulombic
terms (unless maybe some arise due to periodicity, but in that case
you do not have an infinite system and then they are artifacts).
There may be intramolecular terms (like 1-4) or PME-related terms.
-Justin
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey
kgp.a...@gmail.com mailto:kgp.a...@gmail.com
mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote:
I was not sure if changing the size of maxcg would not negatively
influence anything else. I will give it a try. Thanks Justin
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then grompp
worked fine but the mdrun did not start. The
following error
came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 64
/* Verify whether largest charge group is = max cg.*
* This is determined by the type of the local
exclusion
type *
* Exclusions are stored in bits. (If the type is
not large*
* enough, enlarge it, unsigned char - unsigned
short
- unsigned long)*
*/
The solution is described in the comment above.
maxcg = sizeof(t_excl)*8;
Increase the size here.
-Justin
if (nr_in_cg maxcg)
{
gmx_fatal(FARGS,Max #atoms in a charge
group: %d
%d\n,
nr_in_cg,maxcg);
}
-- ====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu http://vt.edu |
(540) 231-9080 tel:%28540%29%20231-9080
tel:%28540%29%20231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
http://vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
====
-- gmx-users mailing list
gmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: [gmx-users] how to simulate a line charge
sorry i did not mention it but the E field contribution should be zero, i am
sure about it. Also when i make all the cutoff = 0 the energy terms are
Step Time Lambda
00.00.0
Energies (kJ/mol)
Bond AngleLJ (SR) Coulomb (SR) Potential
1.11496e-070.0e+000.0e+001.03128e+061.03128e+06
Pressure (bar)
0.0e+00
Step Time Lambda
11.00.0
Energies (kJ/mol)
Bond AngleLJ (SR) Coulomb (SR) Potential
7.49142e-020.0e+000.0e+001.03104e+061.03104e+06
Pressure (bar)
0.0e+00
Coulomb (SR) is quite close but not exactly equal to previous case when
cutoff is 60 nm.
On Sun, Aug 14, 2011 at 1:57 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
Following is the mdp file
cpp = /usr/bin/cpp
;define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 1
;
; Energy minimizing stuff
;
emtol = 200
emstep = 0.01
pbc = no
nstcomm = 0
ns_type = grid
coulombtype = Cut-off rlist = 60
rcoulomb= 60
rvdw= 60
Tcoupl = no
Pcoupl = no
gen_vel = no
E_x = 1 0 0
E_y = 1 0 0
E_z = 1 0 0
Following is the energy term
Step Time Lambda
00.00.0
Energies (kJ/mol)
Bond AngleLJ (SR) Coulomb (SR) Potential
1.11496e-070.0e+000.0e+009.90561e+059.90561e+05
Pressure (bar)
0.0e+00
Step Time Lambda
11.00.0
Energies (kJ/mol)
Bond AngleLJ (SR) Coulomb (SR) Potential
7.55922e-020.0e+000.0e+009.90324e+059.90324e+05
Pressure (bar)
0.0e+00
I suspect that energy terms comes from the use of an electric field, which
you had not mentioned before.
-Justin
Amit
On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Amit Choubey wrote:
Justin, when i define the whole line charge as a charge group i
do get a coulomb energy contribution. I thought there would be
no non-bonded contribution. I use a very high cut-off (longer
than chain length) and no pbc. Am i missing something ?
Without seeing your .mdp file and the actual energy terms you're
observing, I can only guess. One would think that if it is the only
molecule in the system, there should be no intermolecular Coulombic
terms (unless maybe some arise due to periodicity, but in that case
you do not have an infinite system and then they are artifacts).
There may be intramolecular terms (like 1-4) or PME-related terms.
-Justin
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey
kgp.a...@gmail.com mailto:kgp.a...@gmail.com
mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote:
I was not sure if changing the size of maxcg would not
negatively
influence anything else. I will give it a try. Thanks Justin
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote:
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then
grompp
worked fine but the mdrun did not start. The
following error
came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 64
/* Verify whether largest charge group is = max
cg.*
* This is determined by the type of the local
exclusion
type *
* Exclusions are stored in bits. (If the type is
not large*
* enough, enlarge it, unsigned char - unsigned
short
- unsigned long)*
*/
The solution is described in the comment above.
maxcg = sizeof(t_excl)*8;
Increase the size here.
-Justin
if (nr_in_cg maxcg)
{
gmx_fatal(FARGS,Max #atoms in a charge
group: %d
%d\n,
nr_in_cg,maxcg);
Re: [gmx-users] how to simulate a line charge
Amit Choubey wrote: sorry i did not mention it but the E field contribution should be zero, i am sure about it. Also when i make all the cutoff = 0 the energy terms are Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleLJ (SR) Coulomb (SR) Potential 1.11496e-070.0e+000.0e+001.03128e+061.03128e+06 Pressure (bar) 0.0e+00 Step Time Lambda 11.00.0 Energies (kJ/mol) Bond AngleLJ (SR) Coulomb (SR) Potential 7.49142e-020.0e+000.0e+001.03104e+061.03104e+06 Pressure (bar) 0.0e+00 Coulomb (SR) is quite close but not exactly equal to previous case when cutoff is 60 nm. Then I guess in this case you're getting intra-charge group short-range interactions, which I hadn't considered before. In the case of a ridiculously large charge group, atoms may be in the same group but outside the cutoff, in which case they would contribute to Coulomb (SR). Not a typical case. -Justin On Sun, Aug 14, 2011 at 1:57 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Following is the mdp file cpp = /usr/bin/cpp ;define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1 ; ; Energy minimizing stuff ; emtol = 200 emstep = 0.01 pbc = no nstcomm = 0 ns_type = grid coulombtype = Cut-off rlist = 60 rcoulomb= 60 rvdw= 60 Tcoupl = no Pcoupl = no gen_vel = no E_x = 1 0 0 E_y = 1 0 0 E_z = 1 0 0 Following is the energy term Step Time Lambda 00.00.0 Energies (kJ/mol) Bond AngleLJ (SR) Coulomb (SR) Potential 1.11496e-070.0e+000.0e+009.90561e+05 9.90561e+05 Pressure (bar) 0.0e+00 Step Time Lambda 11.00.0 Energies (kJ/mol) Bond AngleLJ (SR) Coulomb (SR) Potential 7.55922e-020.0e+000.0e+009.90324e+05 9.90324e+05 Pressure (bar) 0.0e+00 I suspect that energy terms comes from the use of an electric field, which you had not mentioned before. -Justin Amit On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Justin, when i define the whole line charge as a charge group i do get a coulomb energy contribution. I thought there would be no non-bonded contribution. I use a very high cut-off (longer than chain length) and no pbc. Am i missing something ? Without seeing your .mdp file and the actual energy terms you're observing, I can only guess. One would think that if it is the only molecule in the system, there should be no intermolecular Coulombic terms (unless maybe some arise due to periodicity, but in that case you do not have an infinite system and then they are artifacts). There may be intramolecular terms (like 1-4) or PME-related terms. -Justin On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey kgp.a...@gmail.com mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com mailto:kgp.a...@gmail.com wrote: I was not sure if changing the size of maxcg would not negatively influence anything else. I will give it a try. Thanks Justin On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: I change the maximum charge group size defined in the include/types/nblist.h header
Re: [gmx-users] how to simulate a line charge
I change the maximum charge group size defined in the include/types/nblist.h
header from 32 to 267. Then grompp worked fine but the mdrun did not start.
The following error came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 64
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
In ns.c the relevant section (in bold) is the following:
void init_ns(FILE *fplog,const t_commrec *cr,
gmx_ns_t *ns,t_forcerec *fr,
const gmx_mtop_t *mtop,
matrix box)
{
int mt,icg,nr_in_cg,maxcg,i,j,jcg,ngid,ncg;
t_block *cgs;
char *ptr;
/* Compute largest charge groups size (# atoms) */
nr_in_cg=1;
for(mt=0; mtmtop-nmoltype; mt++) {
cgs = mtop-moltype[mt].cgs;
for (icg=0; (icg cgs-nr); icg++)
{
nr_in_cg=max(nr_in_cg,(int)(cgs-index[icg+1]-cgs-index[icg]));
}
}
* /* Verify whether largest charge group is = max cg.*
* * This is determined by the type of the local exclusion type *
* * Exclusions are stored in bits. (If the type is not large*
* * enough, enlarge it, unsigned char - unsigned short - unsigned
long)*
* */*
*maxcg = sizeof(t_excl)*8;*
*if (nr_in_cg maxcg)*
*{*
*gmx_fatal(FARGS,Max #atoms in a charge group: %d %d\n,*
* nr_in_cg,maxcg);*
*}*
ngid = mtop-groups.grps[egcENER].nr;
snew(ns-bExcludeAlleg,ngid);
for(i=0; ingid; i++) {
ns-bExcludeAlleg[i] = TRUE;
for(j=0; jngid; j++)
{
if (!(fr-egp_flags[i*ngid+j] EGP_EXCL))
{
ns-bExcludeAlleg[i] = FALSE;
}
}
}
if (fr-bGrid) {
/* Grid search */
ns-grid = init_grid(fplog,fr);
init_nsgrid_lists(fr,ngid,ns);
}
else
{
/* Simple search */
snew(ns-ns_buf,ngid);
for(i=0; (ingid); i++)
{
snew(ns-ns_buf[i],SHIFTS);
}
ncg = ncg_mtop(mtop);
snew(ns-simple_aaj,2*ncg);
for(jcg=0; (jcgncg); jcg++)
{
ns-simple_aaj[jcg] = jcg;
ns-simple_aaj[jcg+ncg] = jcg;
}
}
/* Create array that determines whether or not atoms have VdW */
snew(ns-bHaveVdW,fr-ntype);
for(i=0; (ifr-ntype); i++)
{
for(j=0; (jfr-ntype); j++)
{
ns-bHaveVdW[i] = (ns-bHaveVdW[i] ||
(fr-bBHAM ?
((BHAMA(fr-nbfp,fr-ntype,i,j) != 0) ||
(BHAMB(fr-nbfp,fr-ntype,i,j) != 0) ||
(BHAMC(fr-nbfp,fr-ntype,i,j) != 0)) :
((C6(fr-nbfp,fr-ntype,i,j) != 0) ||
(C12(fr-nbfp,fr-ntype,i,j) != 0;
}
}
if (debug)
pr_bvec(debug,0,bHaveVdW,ns-bHaveVdW,fr-ntype,TRUE);
ns-nra_alloc = 0;
ns-bexcl = NULL;
if (!DOMAINDECOMP(cr))
{
/* This could be reduced with particle decomposition */
ns_realloc_natoms(ns,mtop-natoms);
}
ns-nblist_initialized=FALSE;
/* nbr list debug dump */
{
char *ptr=getenv(GMX_DUMP_NL);
if (ptr)
{
ns-dump_nl=strtol(ptr,NULL,10);
if (fplog)
{
fprintf(fplog, GMX_DUMP_NL = %d, ns-dump_nl);
}
}
else
{
ns-dump_nl=0;
}
}
}
Any ideas ?
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Re: [gmx-users] how to simulate a line charge
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then grompp worked fine
but the mdrun did not start. The following error came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 64
/* Verify whether largest charge group is = max cg.*
* This is determined by the type of the local exclusion type *
* Exclusions are stored in bits. (If the type is not large*
* enough, enlarge it, unsigned char - unsigned short - unsigned
long)*
*/
The solution is described in the comment above.
maxcg = sizeof(t_excl)*8;
Increase the size here.
-Justin
if (nr_in_cg maxcg)
{
gmx_fatal(FARGS,Max #atoms in a charge group: %d %d\n,
nr_in_cg,maxcg);
}
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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Re: [gmx-users] how to simulate a line charge
On Sat, Aug 13, 2011 at 05:43, Amit Choubey kgp.a...@gmail.com wrote: The largest charge group contains 267 atoms. The maximum is 32. Column 6 in the [atoms] section of the .top file defines the charge group. If you want each atom to be in its own charge group, you can set this to the same number as the atom number (column 1). Cheers, Bogdan -- gmx-users mailing listgmx-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
Re: [gmx-users] how to simulate a line charge
Thanks Bogdan, defining each atom as a charge group solves the grompp issue. Also here the atoms interact via non-bonded potentials. I think its a better way to simulate the line charge. Amit On Sat, Aug 13, 2011 at 8:29 AM, Bogdan Costescu bcoste...@gmail.comwrote: On Sat, Aug 13, 2011 at 05:43, Amit Choubey kgp.a...@gmail.com wrote: The largest charge group contains 267 atoms. The maximum is 32. Column 6 in the [atoms] section of the .top file defines the charge group. If you want each atom to be in its own charge group, you can set this to the same number as the atom number (column 1). Cheers, Bogdan -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] how to simulate a line charge
I was not sure if changing the size of maxcg would not negatively influence
anything else. I will give it a try. Thanks Justin
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then grompp worked fine but
the mdrun did not start. The following error came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 64
/* Verify whether largest charge group is = max cg.*
* This is determined by the type of the local exclusion type *
* Exclusions are stored in bits. (If the type is not large*
* enough, enlarge it, unsigned char - unsigned short - unsigned
long)*
*/
The solution is described in the comment above.
maxcg = sizeof(t_excl)*8;
Increase the size here.
-Justin
if (nr_in_cg maxcg)
{
gmx_fatal(FARGS,Max #atoms in a charge group: %d %d\n,
nr_in_cg,maxcg);
}
--
==**==
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==**==
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[gmx-users] how to simulate a line charge
Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp I get the following error message. Program grompp_jpt, VERSION 4.5.3 Source code file: grompp.c, line: 175 Fatal error: The largest charge group contains 267 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What should i try to do to circumvent this error. Thanks -- gmx-users mailing listgmx-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
Re: [gmx-users] how to simulate a line charge
Amit Choubey wrote: Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp If you're trying to keep the atoms in a line, the system will not be stable. Angles of 180 degrees routinely crash. files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp I get the following error message. Program grompp_jpt, VERSION 4.5.3 Source code file: grompp.c, line: 175 Fatal error: The largest charge group contains 267 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors What should i try to do to circumvent this error. The maximum charge group size is defined in the include/types/nblist.h header. You can alter the value there, which will get around the error, but consider whether or not this is even a good physical model. If all atoms are in the same charge group, there are no electrostatic interactions between these atoms since neighbor searching is done and short-range energies are calculated based on inter-charge group distances. I have no idea how to properly simulate a line of positively-charged particles, but be aware. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] how to simulate a line charge
On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp If you're trying to keep the atoms in a line, the system will not be stable. Angles of 180 degrees routinely crash. Not even if i use a 3 body angle term with equilibrium angle = 180? If not then why ? files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp I get the following error message. Program grompp_jpt, VERSION 4.5.3 Source code file: grompp.c, line: 175 Fatal error: The largest charge group contains 267 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors What should i try to do to circumvent this error. The maximum charge group size is defined in the include/types/nblist.h header. You can alter the value there, which will get around the error, but consider whether or not this is even a good physical model. If all atoms are in the same charge group, there are no electrostatic interactions between these atoms since neighbor searching is done and short-range energies are calculated based on inter-charge group distances. I have no idea how to properly simulate a line of positively-charged particles, but be aware. Thanks for the pointer and the awareness remark. But since this is a model system and for the physical problem i am trying to deal with its alright if the atoms within the line charge do not interact via non-bonded potentials. -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] how to simulate a line charge
Amit Choubey wrote: On Fri, Aug 12, 2011 at 8:55 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Hi all, I am trying to do a calculation on an artificial line charge in vacuum. The line charge has 267 atoms and each atom has a 1e charge. The atoms are bonded by a bond term and an angle term. I defined the required itp If you're trying to keep the atoms in a line, the system will not be stable. Angles of 180 degrees routinely crash. Not even if i use a 3 body angle term with equilibrium angle = 180? If not then why ? The code has had problems dealing with this case. I do not know if there have been any improvements. The only really stable way to induce linearity is through virtual sites, but I don't know if it is possible to create several hundred virtual interactions defined along a line. -Justin files and top file. When i issue grompp_jpt -v -c parallel.gro -p chain.top -f nve.mdp I get the following error message. Program grompp_jpt, VERSION 4.5.3 Source code file: grompp.c, line: 175 Fatal error: The largest charge group contains 267 atoms. The maximum is 32. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/__Documentation/Errors http://www.gromacs.org/Documentation/Errors What should i try to do to circumvent this error. The maximum charge group size is defined in the include/types/nblist.h header. You can alter the value there, which will get around the error, but consider whether or not this is even a good physical model. If all atoms are in the same charge group, there are no electrostatic interactions between these atoms since neighbor searching is done and short-range energies are calculated based on inter-charge group distances. I have no idea how to properly simulate a line of positively-charged particles, but be aware. Thanks for the pointer and the awareness remark. But since this is a model system and for the physical problem i am trying to deal with its alright if the atoms within the line charge do not interact via non-bonded potentials. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 tel:%28540%29%20231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
