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> 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>> 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>>> 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> | (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>
--
========================================
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 list gmx-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 list gmx-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
--
========================================
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 list gmx-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
