Hi gromacs users,
Is there an especial force field for md simulation of biological systems without water molecules? Or for this purpose, shouldn’t I use the gmx solvate and run the simulation without adding water to the box?
Please guide me about that.
Charges in nonpolarizable, biomolecular force fields are assigned to be overpolarized relative to the gas phase to reflect mean-field polarization response upon interaction with water. As such, none are suitable for simulating without any particular solvent.
Dear Justine,
Thanks for your answer. If I want to simulate a system including polymer and drug molecules in waterless environment, what should I do to get the best results?
Best,
Merry
Rethink not adding the water would be the most obvious suggestion.
Otherwise look at MD packages that can perform implicit solvent simulations, something that (IIRC) hasn’t been available and properly working in GROMACS for years (in part as simulations were slower than with explicit water present).
Or you could maybe try some dual resolution simulations that coarse grain the water and treat the other bits atomistically. But this would again be fiddly and probably slower than just using explicit atomistic water that the models have been parameterised to work properly with.
Cheers
Tom
I guess I should’ve asked why you want to simulate without water?
If it’s for something like calculating a physical property where you need a vacuum simulation then yes just don’t add the water (but you also need to change several mdp settings too).
If it’s because you want another solvent like octanol or cyclohexane then you just need to equilibrate a box of this solvent with an appropriate force field model and then solvate like normal.
And if it’s because you just want to simulate in a vacuum then, for the reasons Justin(e), mentioned you will likely have to develop parameters yourself. One starting place maybe worth looking are the GROMOS “B” sets of force fields as I believe that these are vacuum versions of the corresponding “A” force fields.
Cheers
Tom
Dear Tom, thanks for your answer.
Yes, I need a vacuum simulation. If I don’t add the water molecules, which mdp settings should I change?
It can depend upon exactly what you’re doing the vacuum simulation for. Until you say that, it’s hard to be specific. One of the important things is to use stochastic dynamics.
I want do MD simulation of polymer and drug molecules being in a simulation box in the absence of water molecules. I want to investigate the behavior of polymer and drug molecules (such as their association and aggregation) during the simulation time.
Why without the water though?
As a guess (which is all I can really do without knowing more about what you are trying to do), are you not wanting water because the pure polymer system is typically dehydrated?
If so then you need to build a system structure of the polymer using one of many methods available (gmx insert-molecules, packmol, etc), run an equilibration NPT simulation that will hopefully allow the system to match known properties of the pure polymer system at the simulation temperature (e.g. density). You can subsequently take this equilibrated structure, insert your small molecules of interest (ensuring you have force field parameter compatibility with the polymer model) and away you go.
But as I said, this is just a guess from the information provided. It could be that you’re simply not wanting explicit water to try and speed things up but this isn’t nowadays worth the effort as far as I understand.
Tom
Hello Sir, can you please help me regarding this issue.
Dear @shanza,
Please ask your question in a separate post.
I have asked but didn’t get a reply.
That is why i messeg you here
Dear @shanza,
You should use genion command to neutralize your system. Before that you need to create the required tpr file using grompp command. Check this tutorial:
thank you for replying…
i used the command -maxwarn 1 that you told me and it worked