[gmx-users] gmx insert-molecules not adding the required number of molecules

soumadwip ghosh soumadwipghosh at gmail.com
Wed Nov 30 13:55:21 CET 2016

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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