COM pulling

User discussions
1

GROMACS version: 2018
GROMACS modification: No

Dear all,

I am looking for a way to restrain the center of mass (COM) of two different molecules bathed in water.
The only thing close I found on gromacs that does this is the pull module embedded in the mdp files.
I want to clarify that I want to restrain each molecules (COM) to a different and specific coordinate in my simulated box. Indeed the pull module has an option - pull-coord1-geometry = direction, where I can set the origin (pull-coord1-origin= 0 0 0, for example) and a vector directing the movement of the COM (pull-coord1-vec= 1 1 1) with time (pull-coord1-rate = 0.1nm/ps). However I don’t want my COM to move in time, I want it stationary in a specific coordinate throughout my entire simulation time. I see that I can set a parameter - pull-coord1-start = no - so that it doesn’t start moving towards my vector and stays in what I labeled “origin”.

With all that said, when running my simulations, it looks like my specification in the mdp file lead to no restraints, and it looks like my molecules defuse freely without an energetic bias towards my specified origin coordinate. Here are my mdp settings:

pull = yes
pull-ngroups = 2
pull-group1-name = MEO
pull-group2-name = AGLC
pull-ncoords = 2

pull-coord1-type = umbrella
pull-coord1-geometry = direction
pull-coord1-groups = 0 1
pull-coord1-dim = Y Y Y
pull-coord1-origin = 3.75 2.5 2.5
pull-coord1-vec = 1.0 1.0 1.0
pull-coord1-k = 10000.0
pull-coord1-rate = 0.0
pull-coord1-init = 0
pull-coord1-start = no

pull-coord2-type = umbrella
pull-coord2-geometry = direction
pull-coord2-groups = 0 2
pull-coord2-dim = Y Y Y
pull-coord2-origin = 3.75 2.5 2.5
pull-coord2-vec = 1.0 1.0 1.0
pull-coord2-k = 10000.0
pull-coord2-rate = 0.0
pull-coord2-init = 0
pull-coord2-start = no

where pull-coord2-init = 0 is supposedly irrelevant to the “direction” type of pulling.

If anybody has any experience with this pulling direction technique and might point me to where my settings are wrong, Id be extremely thankful.

Best to all,
Ilan Shumilin

2

Hi,
I understood that you want to restrain the COM of each molecules to a different coordinate, but in the mdp setting you have the same pull-coord1-origin = pull-coord2-origin = 3.75 2.5 2.5.

An alternative approach is to constraint the distance between the center of mass of the two proteins using the pull code with the following options.
pull-coord1-type = constraint
pull-coord1-geometry = distance

Best regards
Alessandra

3

Dear Alessandra,

Thank you for your reply.
I intended to restrain the COM of both molecules to the same coordinate, because one is cyclic and can complex the other one. I also want them to remain in the same place in my box, so distance restraint doesn’t help in my case.

Best regards,
Ilan

4

Hi Ilian,
What do you mean with “when running my simulations, it looks like my specification in the mdp file lead to no restraints, and it looks like my molecules defuse freely without an energetic bias towards my specified origin coordinate.”
Are the two molecules moving apart from each other? Or do they just translate?
What does md.log report? You can also plot molecule c.o.m in function time, to understand better what happen.

Do you have the same problem if you fix the com of only one molecule?

Best regards
Alessandra

5

Hi Alevilla,

The two molecules translate freely in all direction. The directions of pulling dont affect their trajectory.
I have the same problem for one molecule.

Thanks,
Ilan

6

Hi,
In the case of molecule, is the molecule that translates or is the whole box that translates?
Best regards
Alessandra

7

Hi Alessandra,
The molecule translates.

8

Hi,
Do you get any error in the pre-processing? I quickly tried your pull setting in NPT and NVT ensemble for one protein-in-solution system using 2020.3. Those two extra options were necessary in my case
pull-pbc-ref-prev-step-com
pull-group1-pbcatom

Kind regards
Alessandra