Thank you
On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Warren Gallin wrote:
You are not specifying the ions to be added using the -pname and
-nname options with the genion command.
Perhaps that is a problem?
They are not necessary; the default names are used and should be
correct for all force fields now that naming has been standardized.
Thus far I have seen no evidence that genion is not doing what it is
supposed to. It reports finding a net -50 charge on the system.
What happens then? Does the output coordinate file contain ions?
The topology will not be modified because genion is not being told
to (i.e. through the use of -p).
-Justin
Warren Gallin
On 2011-07-26, at 2:49 PM, Sara baretller wrote:
thanks but i want to neutralize the system , why genion -s
file.tpr -conc 0.2 -neutral -o file.gro -random does not
neutralize the system to 0 .
On Tue, Jul 26, 2011 at 3:48 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote:
Sara baretller wrote:
Hi
this a part of the md.log where the system has -50 charge
two-body bonded interactions: 0.407 nm, Bond, atoms 514 515
multi-body bonded interactions: 0.731 nm, G96Angle, atoms
1272 1275
Minimum cell size due to bonded interactions: 0.804 nm
Maximum distance for 9 constraints, at 120 deg. angles,
all-trans: 0.810 nm
Estimated maximum distance required for P-LINCS: 0.810 nm
This distance will limit the DD cell size, you can override
this with -rcon
Optimizing the DD grid for 4 cells with a minimum initial
size of 0.810 nm
The maximum allowed number of cells is: X 11 Y 11 Z 11
Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Using shifted Lennard-Jones, switch between 0.9 and 1.2 nm
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge: -50.000
Generated table with 1100 data points for Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ6Shift.
Tabscale = 500 points/nm
Generated table with 1100 data points for LJ12Shift.
Tabscale = 500 points/nm
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing ia32 SSE2 support... present
There's nothing abnormal here. genion reports that it finds
a -50 charge on the system. That's what it's supposed to
do. Based on what it finds in the topology, it adds
neutralizing ions and any additional ions to reach the
specified concentration. You only have a problem if grompp
later complains that there's still some residual charge
(excluding tiny rounding discrepancies).
-Justin
On Tue, Jul 26, 2011 at 2:18 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Sara baretller wrote:
Hi All
I used the genion command using like this "genion -s
file.tpr
-conc 0.2 -neutral -o file.gro -random " again and i
checked
the md.log file and it says that the net charge is
negative like
it was before using the genion command.
so can anybody tell me what is wrong with the line
genion -s
file.tpr -conc 0.2 -neutral -o file.gro -random .
Please copy and paste the exact (pertinent) output from
the log file.
-Justin
Sara
On Tue, Jul 26, 2011 at 1:05 PM, 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:
Sara baretller wrote:
Hi all
I used the genion to add a concentration and to
neutalize the
system in the same time by using the
*genion -s file.tpr -conc 0.2 -neutral -o
file.gro
-random
so it did add the NA and Cl but it did not
neutralize the
system, the net charge of the system still the
same negative.
I find this hard to believe. The application of
genion -conc
-neutral has worked in every instance I've tried it
along every
Gromacs version. Check your output again.
so i tried to use the genion seperate to
neutralize the
charge using the file.tpr and out file as the
file.gro, however it reset the file.gro
and i lose the NA And
CL ions
added for the concentration.
Without the actual sequence of commands, this is
not a useful
description. genion adds ions based on whatever it
finds in
the .tpr
file (which is presumably not neutralized). If you
do not
re-create
a .tpr file in between different additions of ions,
you're
going to
be undoing work you thought you did.
-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> <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://vt.edu/Pages/Personal/__justin
<http://vt.edu/Pages/Personal/justin>>
<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>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>__>
http://lists.gromacs.org/______mailman/listinfo/gmx-users
<http://lists.gromacs.org/____mailman/listinfo/gmx-users>
<http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>>
<http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<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>
<http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>>
<http://www.gromacs.org/____Support/Mailing_Lists/Search
<http://www.gromacs.org/__Support/Mailing_Lists/Search>
<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>
<mailto:gmx-users-request@__gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-request@
<mailto:gmx-users-request@>__gr__omacs.org <http://gromacs.org>
<mailto:gmx-users-request@__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>
<http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>>
<http://www.gromacs.org/____Support/Mailing_Lists
<http://www.gromacs.org/__Support/Mailing_Lists>
<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 <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>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/____mailman/listinfo/gmx-users
<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
<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>
<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>
<mailto:gmx-users-request@__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>
<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 <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 list gmx-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>
--
gmx-users mailing list gmx-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 <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 list gmx-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>
