[gmx-users] confout.gro

[RINU KHATTRI]

hello
the command is gmx grompp when i am running
gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
No command 'gmx' found, did you mean:
 Command 'gm' from package 'graphicsmagick' (universe)
 Command 'pmx' from package 'pmx' (universe)
 Command 'ngmx' from package 'gromacs' (universe)
 Command 'gcx' from package 'gcx' (universe)
gmx: command not found
mtechbio at mtechbio-HP-Z400-Workstation:~/Desktop/fresh1$ gmx  grompp -f
ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr
No command 'gmx' found, did you mean:
 Command 'gm' from package 'graphicsmagick' (universe)
 Command 'pmx' from package 'pmx' (universe)
 Command 'ngmx' from package 'gromacs' (universe)
 Command 'gcx' from package 'gcx' (universe)
gmx: command not found
help


On Mon, Jul 7, 2014 at 3:47 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> hello gmx users
> i am also getting that error
> [file topol.top, line 24832]:
>   System has non-zero total charge: 14.788998
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer
>
>
> On Mon, Jul 7, 2014 at 2:47 PM, RINU KHATTRI <nickname.mittu at gmail.com>
> wrote:
>
>> hello gromacs users
>> i am applying (solv.gro 101917-108573 topol.top )/3
>> =     i have to subtract 2218.66 into old figure (32672 which is present
>> in topol.top )
>> due to float no still error persist only one coordinate is different
>> Fatal error:
>> number of coordinates in coordinate file (solv.gro, 101917)
>>              does not match topology (topol.top, 101916)
>> how to resolve
>> i have been apply all the numbers in float but still difference
>> help
>>
>>
>> On Mon, Jul 7, 2014 at 2:06 PM, RINU KHATTRI <nickname.mittu at gmail.com>
>> wrote:
>>
>>> hello everyone
>>> after this step now i am in the
>>>  grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
>>> step but after running i got error
>>> Fatal error:
>>> number of coordinates in coordinate file (solv.gro, 101917)  does not
>>> match topology (topol.top, 604599)
>>> i have been edited the sol (counted from solv.gro) but still error how
>>> to resolve it infact figure is increased
>>>
>>>
>>>
>>> On Mon, Jul 7, 2014 at 12:05 PM, RINU KHATTRI <nickname.mittu at gmail.com>
>>> wrote:
>>>
>>>> hello gromacs users
>>>> thanks justin i have applied
>>>>
>>>> perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat
>>>>
>>>> mdrun -v -deffnm em
>>>>
>>>> perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
>>>> area_shrink1.dat
>>>>
>>>> after that solvation step but no command is present in dppc tutorial
>>>> should i used
>>>>
>>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>>>
>>>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>>>
>>>> but conf.gro is the combined file of (b3_procesed.gro+ drg.itp)
>>>>
>>>> is it this file or em.gro which is formed 2 step before this
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Sat, Jul 5, 2014 at 4:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>>
>>>>>
>>>>> On 7/5/14, 12:51 AM, RINU KHATTRI wrote:
>>>>>
>>>>>> hello gromacs users
>>>>>> but i am confussed if confout.gro is input, in which step it is formed
>>>>>> according to tutorial before this step the step is
>>>>>> perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat
>>>>>> is system_inflated.gro is confout.gro or which gro file i must be used
>>>>>> as confout.gro
>>>>>>
>>>>>> perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5
>>>>>> area_shrink1.dat
>>>>>>
>>>>>
>>>>> The file "confout.gro" is the default name of the final output
>>>>> coordinates of an mdrun process, unless you provide a different file name
>>>>> to mdrun -c.  In this case, the protocol is:
>>>>>
>>>>> 1. Inflate the system (produce system_inflated.gro)
>>>>> 2. Minimize the inflated system (produce confout.gro, unless otherwise
>>>>> named)
>>>>> 3. Begin shrinking the system, starting with the output of step 2.
>>>>>
>>>>> So "confout.gro" is the _output_ of step 2 and the _input_ of step 3.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 601
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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>>>>>
>>>>
>>>>
>>>
>>
>