How to insert different molecules into system?

User discussions
1

GROMACS version: 2024.3
GROMACS modification: No

Hi,

I’ve tried to insert several molecules into system. I’ve seen example for one kind molecule with 128 nmol like this: gmx insert-molecules -ci DPPC-em.gro -box 7.5 7.5 7.5 -nmol 128 -radius 0.21 -o 128_noW.gro

If I want to insert multiple molecules with different -nmol into a system, could you tell me how to do that in GROMACS?

Thank you!

2

Hi @Scola ,

just repeat the procedure with gmx insert-molecules by providing with the flag -f the box to which you want to add to other molecules. Take a look at the manual.

Just to give an example, if I wanted to have a box of side 5nm with 10 molecules of type A, 15 of type B, and 1000 of type C, I would do

# generate box of side 5 with 10 molecules of type A
gmx insert-molecules -ci A.gro -box 5 5 5 -nmol 10 -o box_with_A.gro
# add to the previous output the molecules of type B
gmx insert-molecules -ci B.gro -nmol 15 -f box_with_A.gro -o box_with_AB.gro
# add those of type C
gmx insert-molecules -ci C.gro -nmol 1000 -f box_with_AB.gro -o box_with_ABC.gro

Note how the output of the previous command is used as input structure for the following. At the end, box_with_ABC.gro will have the molecules requested (provided there was enough space to add them all).

3

That’s great! Thank you for the guidance!

4

Hi @obZehn ,
When I run the command, I wonder what is a good number for parameter -radius.

Could you tell me if there are any criteria for choosing the number?

The molecules that I’m working on are fatty acids, such as decanoic acid. (10 carbon chain)

Thank you!

5

I actually never used the -radius flag. I would just go without it and see if everything works as expected before fine tuning the parameter!

6

Thanks for the guidance!

I also want to add some ions to the system, e.g. Br- and Na+.

Can I use the gmx insert-molecules to do that or I have to use gmx genion?

7

This really comes down to your preference, but for simple mono-atomic ions I see no reasons for using gmx insert-molecules. If you know the amount of ions you have to add, e.g. your protein has charge -1 and you just want to insert 1 Na+ to neutralize the system, then insert-molecules is okay, but you have to provide the structure file as input. On the other hand, genion does everything for you, that is, it removes solvent molecules, add the right amount of salt with the naming you want, updates the topology, etc. Overall, stick to genion if you really have no good reason to use other tools (larger salts, for example).

8

Thanks for the advice!