[gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program
Hi , I'm using mdrun-gpu for testing gpubench demos. But I've got this error message: Fatal error: reading tpx file (topol.tpr) version 73 with version 71 program I installed different version of gromacs 4.5 to 4.5.4 and gpu-gromacs-beta 1, 2 versions. But it still doesn't work. any idea on this? 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] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program
H.Ghorbanfekr wrote: Hi , I'm using mdrun-gpu for testing gpubench demos. But I've got this error message: Fatal error: reading tpx file (topol.tpr) version 73 with version 71 program I installed different version of gromacs 4.5 to 4.5.4 and gpu-gromacs-beta 1, 2 versions. But it still doesn't work. any idea on this? Gromacs programs are backwards-compatible, but if the .tpr file version has changed between revisions, they are not forward-compatible. A version 73 .tpr file is from Gromacs version 4.5.4, so the error comes when you try to use an older Gromacs version to run it. Stick with one version of Gromacs (preferrably the newest) and use it for everything. Having multiple versions lying around unnecessarily can be problematic when you might wind up using executables from different installations. -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] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program
I used the newest version of gromacs 4.5.4 (and not install beta gpu version ) so everything goes well. thanks for your reply On Sun, Aug 14, 2011 at 5:52 PM, Justin A. Lemkul jalem...@vt.edu wrote: H.Ghorbanfekr wrote: Hi , I'm using mdrun-gpu for testing gpubench demos. But I've got this error message: Fatal error: reading tpx file (topol.tpr) version 73 with version 71 program I installed different version of gromacs 4.5 to 4.5.4 and gpu-gromacs-beta 1, 2 versions. But it still doesn't work. any idea on this? Gromacs programs are backwards-compatible, but if the .tpr file version has changed between revisions, they are not forward-compatible. A version 73 .tpr file is from Gromacs version 4.5.4, so the error comes when you try to use an older Gromacs version to run it. Stick with one version of Gromacs (preferrably the newest) and use it for everything. Having multiple versions lying around unnecessarily can be problematic when you might wind up using executables from different installations. -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
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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mailto:gmx-users@gromacs.org
http://lists.gromacs.org/__mailman/listinfo/gmx-users
http://lists.gromacs.org/mailman/listinfo/gmx-users
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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
--
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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
==**__==
-- gmx-users mailing listgmx-users@gromacs.org
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before
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Please don't post (un)subscribe requests to the list. Use the
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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
[gmx-users] Compute Intensive benchmarks for Gromacs
Dear All, I would like to use Gromacs on a cluster of machines. I am not aware for technicalities of Gromacs, but I am looking for large problem size which can utilize my cluster resources, and should be able to create enough imbalance in the computations. The purpose is for bench-marking the cluster, and for analyzing system architecture level details for imabalance caused when jobs are made to run on magnitude of machines. Any help regarding getting such benchmarks will be highly appreciated. Thanks in Advance. Best regards, Rajat -- 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] negative dihedral cp (during cgenff conversion)
Random noob question: Should the cp field (field 7) in [ dihedraltypes ] always be positive or can it be negative? In the CGenFF conversion, the CHARMM dihedral has: OG302 CG2O2 CG321 CG331 -0.1500 1 180.00 ! LIPID methyl proprionate when I convert to gromacs: [ dihedraltypes ] ; i j k l funcphi0cp mult OG302 CG2O2 CG321 CG331 9 180.0 -0.627601 ;LIPID methyl prop This is the only instance I have seen of a negative number for the dihedral term, so I wonder what the right way to handle it is... (I suppose I could just run it and see...) -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | BEC 257 Genetics, Div. of Research | 1150 10th Avenue South p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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
