Vacuum Simulations

User discussions
1

GROMACS version: 2018
GROMACS modification: No

Hello, I am a new user for GROMACS and I am trying to run a vacuum simulation of a protein. Besides skipping the solvation and adding ions commands of a regular simulation, what else needs to be done in terms of .mdp files to accomplish this task?
Thank you

2

One of the main things is you need to run it at constant volume i.e. no pressure coupling. Otherwise the box will simply collapse.

You also need to ensure that the settings are appropriate for the vacuum forcefield that you are using.

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3

Thank you very much and understood- so then would I also skip NPT equilibiration altogether? Just want to confirm.

4

Yes, otherwise your box will compress into a liquid.

Also relevant - formally, a vacuum simulation is performed with no PBC and infinite cutoffs, but GROMACS doesn’t support such calculations, so one can instead use a very large box, NVT ensemble, and long cutoffs.

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5

I am simulating (C60 and TAPC) molecules in vacuum and I have a question please. If I inserted my molecules in a very large box, my molecules will not be packed, they will be distributed along the whole box which in turn will affect the density measurements along the z axis using gmx density. Is there any way to avoid that ?

6

@M_Abdelaal, If you have multiple molecules in a box, It is no more Gas/Vacuum simulation. According gas phase/vacuum definition, There should not be any intermolecular interactions.In gas phase, Molecules will experience only stochastic collisions for a given temperature. So if you have multiple molecules, it is no more true. Besides, You might try -pbc whole and -trans to position whole molecule for density calculation.

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7

@Masrul that is true for an ideal gas but multiple molecules can interact in vacuum.

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8

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

9

hi jelemkul,

Could you pls give me some advice about my question?

10

Hello I am a new user to GROMACS, I am performing md simulation for a protein for my dissertation thesis, can anyone please guide me what factors should be eliminated during vacuum simulations?