[gmx-users] confout.gro

[Justin Lemkul]

On 7/7/14, 6:34 AM, RINU KHATTRI wrote:
> 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
>

As announced this morning, I am upgrading the tutorials to be compatible with 
Gromacs version 5.0, so the syntax of commands is slightly different.  Leave off 
"gmx" if you're using an older version.

-Justin

>
> 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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>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>

-- 
==================================================

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

==================================================