How to simulate protein in vacuum in Gromacs 2021.4

User discussions
1

GROMACS version:2021.4

Hi,
I am a beginner in Gromacs, now I have a basic question about the protein simulation in vacuum.

Q;
I want to simulate the protein in vacuum and water condition respectively to test the effects of water to protein. The protein can be obtained from PDB, (xRay method), and it has 14 negative charges.

  1. what should I do to modify the protein before I put it into the box?
    As I know, protein should not be charged in vacuum condition, while the data of PDB was experimented in physiology conditions. Must I neutralize the protein before I put it into the box? and how?

  2. what is the meaning of vacuum in gromacs? Is it no water molecules in the box? (just generate a box and do not solvate it?)
    I did not search any valuable procedures about this part, so I am here asking for some advice.

  3. which one might be the most suitable forcefield to conduct this MD run?

Regards,
CJ_Yin

2

A vacuum simulation in GROMACS can only be accomplished by centering your solute in a very large box (filled with nothing) and using an NVT ensemble. There are no “true” options for simulating in vacuo, e.g. without periodicity.

None of the force fields in GROMACS are designed to be used in vacuo. They are all intrinsically over-polarized to represent condensed-phase, aqueous behavior. I would be very skeptical of any result of such a simulation.

1 Like
3

Thanks for your patient reply.

I read some papers which used vacuum condition to study the water effects to protein structure
For example, Sweat-Resistant Silk Fibroin-Based Double Network Hydrogel Adhesives and DOI:10.1080/07391102.2017.1323015.

However, both of them did not show how to realize vacuum simulation. And they did not set large box neither.

In another group (Eur. Biophys. J. 40,843, 2011), they proposed the force field GROMOS54B7 for simulating in vacuo. But it is difficult for me to install that force field.