Adding a big thing, then lots of small things randomly and then lots of
medium sized things randomly isn't going to work very well to give you
something approximately close-packed at the end. You're just not likely to
end up with exactly enough holes suitable for things of medium size. So
work from biggest to smallest. You may find you want to play with the radii
of urea atoms to get the right number to insert (into holes nominally too
small for them), and then very gentle equilibration to start off with.
On Wed, Nov 30, 2016 at 1:56 PM soumadwip ghosh <soumadwipgh...@gmail.com>
> Hi all,
> I have recently been looking at the dynamics of protein in
> presence of urea+osmolyte. The protein I have taken is a chicken villin
> headpiece subdomain (HP-36). It is inside a cubic box of 141 nm3 volume. 8M
> urea corresponding to this box volume = 680 number of urea molecules and I
> want the osmolyte to be in half of its molarity. Thus, the required number
> of osmolyte is 340. Previously, I have worked with 1:5 molar ratio of
> urea:osmolyte and it proceeds without any difficulty. This time what I
> encounter is:
> 1. 680 number of urea molecules goes inside the protein box using gmx
> insert-molecules command without any difficulty.
> 2. When I call the same command for inserting my osmolyte (340 in number)
> it can only insert 220 molecules even with the -nmol x, -try x option.
> 3. If I try to insert a random number of osmolytes (say 500) it takes a
> long time for gmx insert-molecules before printing the execution has been
> 'killed' and it does not generate any output file.
> 4. If I try a bigger box, then the required number of species increases and
> I face the same problem with my osmolyte even though urea addition is
> What is happening here? Is there a way to play around with the gmx
> insert-molecules/genbox command to obtain the desired number of molecules
> inside a box of known dimensions in which something already resides (in my
> case protein+8M urea). I shall be obliged if someone helps me out with this
> P.S: I am using GROMACS 5.0.4 in combination with OPLS-AA force field.
> Thnaks and regards,
> Soumadwip Ghosh
> Research Associate
> Indian Institute of Technology Bombay
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