[gmx-users] confout.gro

[RINU KHATTRI]

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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