Hello everyone,
I’ve tried to generate a solvent box with the hexane residue already present in the force field, but I can’t even energy minimize it.
You need to provide more details than that, it provides no information people can use to try and assist you.
Provide things like the procedure you use, each of the steps, the actual command lines used (copy and paste), and the actual output that shows the error(s) (copy and paste).
I have simply solvated a cubic box with hexane (gmx solvate) using the Drude polarizable force field. I think the problem is the ff itself, cannot take into account solvent different from water. The problem is already in the energy minimization phase cause I have high potential energy and an uncomplete em that causes trouble in the following nvt phase, so dd decomposition and so on…
You’re leaving out a ton of information here. Where did you acquire the coordinates? How did you generate the topology? Did you do a proper additive equilibration before converting the coordinates to Drude? It is easy enough to break a nonpolarizable simulation, it’s even easier to break a polarizable one.
I’m not even sure what this means, but we have tons of small molecules in the force field that can be used as liquid solvents. They work fine. The problem almost certainly comes from your preparation, and you need to provide more details about all the steps you’ve taken, including exact commands, sources of coordinates, etc.
First of all, thank you for the reply
Coordinates and topology are from the pdb2gmx, I have generated the input .pdb through ATB. What do you mean by additive equilibration?
You need to equilibrate the coordinates using a nonpolarizable force field first (use CHARMM). Right now, you’ve got a box of random hexane molecules that may or may not be energetically reasonable under any force field. It’s not surprising that the Drude minimization fails. You have to prepare the systems very carefully.
We’re going to have some resources out on this soon - I have a methodological book chapter in press and we are preparing some new CHARMM-GUI features that will make GROMACS use easier, but please understand that right now, the current status of the code is that it’s really only accessible to experts. If you’re not well versed in polarizable simulations, and this kind of advice that I’m giving is new to you, please spend a bit of time reading our published papers to see how we prepare systems.
Ok, thank you for the input.
Hi Justin,
I have done what you suggested and single equilibrations go fine, but I have a doubt:
I cannot do serial NVT and NPT equilibration cause of I have no shell position?
there are shells that are connected to particles outside their own charge group, will not predict shells positions during the run
Shell prediction is not relevant with our Drude model. It is most useful for massless shell simulations with SCF.