[gmx-users] Problem with small number of water molecules

Justin Lemkul jalemkul at vt.edu
Tue Mar 11 19:13:47 CET 2014

On 3/11/14, 2:03 PM, ehs wrote:
> Hi gmx users,
> I have tried many ways to simulate a relatively long ionomer chain (340
> atoms) solvated in about 100 water molecules, but I did not succeeded yet.
> The ionomer length is mainly in x direction. For instance, I used the
> following commands:
>    editconf_d -f conf.gro -bt dodecahedron -box 2 1 1 -d 0.5 -o box.gro
>    genbox_d -cp box.gro -cs spc216.gro  -p topol.top -o sol.gro
> The number of SOL molecules added is 94. However, it is uniformly
> distributed in the box and only exists in the central region of the box. I
> ran the energy minimization using sol.gro, but it does not converge to
> Fmax<100. I checked the output file and it seems that all SOL molecules have
> been shifted to left corner of the box. I hope somebody could help me.

That's how genbox works.  It tiles the solvent coordinate file starting at the 
coordinate origin until the box is full or a maximum number of waters have been 
added.  I don't see how the above commands would limit the number of waters to 
94.  Have you provided the exact commands?  Are you using -maxsol?



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


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