[gmx-users] (no subject)

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 26 23:03:24 CEST 2011 


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)
>>
>>        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>>
>>
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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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-- 
========================================

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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