[gmx-users] (no subject)
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 27 00:07:46 CEST 2011
Sara baretller wrote:
> hi all
>
> yes the gro file does have all ions, NA + number of ions equal to CL
> number. so when i use grep command , i have same number of NA and CL and
> that what tells me that something is wrong , because i should have
> another 50 ions of NA extra to neutralize the system
>
I've never seen genion do anything like this. If you send me your .tpr file
(off-list) I will see if I can uncover what's going on. I also need to know
which Gromacs version you're using.
-Justin
> Thank you
>
>
>
> On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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>
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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 <http://vt.edu> <http://vt.edu> | (540)
> 231-9080 <tel:%28540%29%20231-9080>
> <tel:%28540%29%20231-9080>
>
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> <http://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 <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 <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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