[gmx-users] confout.gro

[RINU KHATTRI]

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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>
>