[gmx-users] Adding urea molecules to lysozyme simulation

[Justin Lemkul]

On 9/2/15 4:04 PM, Martin Nors Pedersen wrote:
> Hello Everyone,
>
> I have completed the very nice tutorial for lyzosyme available here:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
>
>
> As I am working with unfolding, I would like to try simulate the unfolding by
> adding urea. I have made a urea.gro file (lifting the coordinates from 3va7.pdb)
> and wanted to use the gmx insert-molecules command to insert 300 copies of it.
> my procedure was the following:
>
> convert pdb file to gro file using gmx pdb2gro, selecting OPLS/AA force field
> and the tip4p water model
> create a box using: gmx editconf -f lys.gro -o lysBox.gro -c -d 1.0 -bt cubic
> solvate using: gmx solvate -cp lysBox.gro -cs spc216.gro -o lysSolv.gro -p
> topol.top
> add the urea molecules: grm insert-molecules -f lysSolv.gro  -ci urea.gro -nmol
> 300 -o lysUrea.gro
>
> this gives me the error message:
> Table routines are used for coulomb: FALSE
>
> Table routines are used for vdw:     FALSE
>
> Cut-off's:   NS: 0.3078   Coulomb: 0.3078   LJ: 0.3078
>
> System total charge: 0.000
>
> Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Coulomb 0e+00
>
>
> Grid: 23 x 23 x 23 cells
>
> nri = 33186, nrj = 209128
>
> Try 1143box_margin = 0.2907erlap:
>
> Neighborsearching with a cut-off of 0.3078
>
>
> NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
>
> removed in a future release when 'verlet' supports all interaction forms.
>
>
> NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
>
> removed in a future release when 'verlet' supports all interaction forms.
>
> The same is the case if the urea is attempted added to lysBox.gro instead of
> lysSolv (so to the box with lyzosyme before I have added solvent).
>
> Can anyone give me any help with what my problem is? I guess one problem could
> be if I ask gromacs to insert urea, where another molecule is already
> positioned. Ideally, I would like to replace some water molecules with urea, but
> I am not sure how to do that.
>

None of the above is an error.  You should be adding the urea before water; 
trying to do it afterwards won't work due to lack of available space.  There is 
no mechanism currently to replace waters with other polyatomic species.  See:

http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents

-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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