[gmx-users] Solvate with water

[Justin Lemkul]

On 7/17/16 6:11 AM, roshanak starlight wrote:
> hello i,m trying simulation kalp-15 in dppc by tutorial that is in this
> website:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein_old/03_solvate.html
>  i reach to 'solvate with water' in step 3 .
> 1. i want to know ,is this command true ?
> $ genbox -cp system_shrink26.gro -cs spc216.gro -vdwd  -o
> system-solvated.gro

No, because -vdwd takes a real number argument.  But it's not needed.  The 
bigger issue is why you are following on old tutorial (one that I should have 
taken offline long ago and shouldn't actually be linked from anything) to learn 
about GROMACS.  Use the new version; it's the one I keep updated and that has 
current GROMACS syntax.

Note, though, that the membrane protein tutorial assumes the user knows how to 
do the "easy" stuff like solvating, adding ions, etc. and will not provide every 
single command.  There are other tutorials explaining all of that, which you 
should work through and understand before trying the harder stuff.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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