[gmx-users] (no subject)
Sara baretller
sarabiocomputation at gmail.com
Tue Jul 26 23:41:19 CEST 2011
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
Thank you
On Tue, Jul 26, 2011 at 5:03 PM, Justin A. Lemkul <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>
>>> 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>> 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>>> 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)
>>>
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>>> ICTAS Doctoral Scholar
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>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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