[gmx-users] generating tripeptides in a box

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 30 19:12:52 CEST 2012

Hi Pim,

I know the problem and also think the problem lies within genbox, but I
haven't been able to trace it. A workaround is to solvate with a small box
containing a single water moleule.



On Aug 30, 2012 6:12 PM, "Pim Frederix" <pim.frederix at strath.ac.uk> wrote:

Hello users,

I'm experiencing trouble using genbox for creating a box of tripeptides in
MARTINI CG polarizable water. I feel like any of the options below should
do the trick, but all give (different) problems.

Generating the randomly place tripeptide box works fine, nothing unusual
about the output:

genbox -ci tripeptide.pdb -box 12.5 12.5 12.5 -vdwd 0.3 -nmol 300 -o

> In which tripeptide.pdb is the coarse-grain coordinates generated either
with Martini 2.1 or Martini 2.2P (martinize.py)

But then trouble starts.
I have got the polarizable water from the Martini website (also normal,
single bead water gives problems in method 1&2, seems to work ok for method

1) genbox -cp tripeptide_box.gro -cs polarize-water.gro -vdwd 0.21 -o
tripeptide_water.gro     (vdwd 0.21 is needed for Martini water)
This gives me a result that looked fine at first, until I realised that
somehow a simulation box that has a greater density of water molecules in
the centre of the box. It's hard to describe, but it looks like a cubic
water box with high density in the middle of a normal cubic water box.
There's no gradual gradient, it stops at a certain distance. Hopefully this
ASCII art side view will help:
|   __   |
|  |__|  |

If I try to minimize/equilibrate this box it just explodes, as the density
in the center is about twice the appropriate density.

2) I though this may be because the water box is not large enough (it's
about 5x8x5 nm, my system 12.5x12.5x12.5). However, firstly generating a
solvent box that is large enough to cover my whole tripeptide box, using
genconf, doesn't help and gets me back to the same problem as in 1)

3) I discovered that with the single-bead water it works if I make a water
box that is exactly the size of the tripeptide box, the problem is minute
and gets annihilated by just minimizing and equilibrating the box. However,
if I do this with the polarizable water (3 'beads' per water molecule) this
doesn't work anymore. I get my solvated box with the right density, but
there are a few water molecules (it varied from about 2 to 10 in a small
number of attempts)  that are completely out of the box some 10 nm away.
Manually removing them is not an option unfortunately as I need to automate
this process for a large number of peptides.
Also, if I get the number of waters from the residue information and put in
the topology file, the number of coordinates in the .gro file doesn't match
the number of coordinates in the .top, there's a varying mismatch of around
100 atoms (out of ~17000).

I've posted this problem about 2 years ago as well, but didn't get any
replies except from people that wanted to know if I solved the problem
already. So I really hope someone can make sense of this and tell me where
it's going wrong (either genbox (which I think) or something to do with the
Martini molecules) and can suggest something to solve it. I'm happy to send
files if needed.

Many thanks,

Pim F.
University of Strathclyde
Glasgow, UK

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