[gmx-users] confout.gro

[RINU KHATTRI]

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
>>>>
>>>> ==================================================
>>>>
>>>> --
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>>>
>>>
>>
>