[gmx-users] confout.gro

[Justin Lemkul]

On 7/7/14, 2:35 AM, RINU KHATTRI 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
>

The shrinking steps are done iteratively.  You should not be using editconf, 
genbox, or anything else until you have achieved a suitably compact membrane. 
This is stated explicitly in the tutorial.  After shrinking, run EM, then shrink 
again, EM, shrink... until you achieve a reasonable APL value.  Then and only 
then should you proceed to solvating, adding ions etc (with no manipulation of 
the box by editconf).

-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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