GROMACS version: 2019.4
GROMACS modification: No
Here post your question
I am calculating the PMF for two sheets in solution with different interlayer distances (see figures below). The problem is when sheets are in a certain range (between 0.5 to 0.65 nm) they will move toward each other so the distance will be decreased to 0.4 nm so there will not be any window for this range. The results are shown in the figure below.
The question is how can I sample from this range which is not stable and sheets will absorb each other?
More info: I restrained one sheet, the other sheet is free but there’s an umbrella potential between two sheets. Th epull_coord1_k is 1000. Changing k doesn’t help too. Using “pull coord1_type = constraint” will deform the free sheet heavily.
Hello, have you solved this question? I also met this question and want some answers.
I pull one sheet along z axis, when I select some conf.gro to execute US, the upper sheet would decrese heavily so that go to the original position. I can’t calculate the PMF when this situation appeared.
Thank you
Thanks a lot for your answer.
I have read some articles about peeling one sheet to achieve exfoliation and calculating the PMF along the z axis. They usually use ABF from lammps. Why US from GROMACS can not achieve this calculation? https://pubs.rsc.org/en/content/articlelanding/2019/CP/C9CP03654G#!divAbstract
Best regards
I’m not familiar with ABF, and I’m not sure about the reason behind this but I think it has something to do with the force required to exfoliate sheets in this direction. Whatever the reason is, I couldn’t calculate PMF either with US or AWH method.
You’re welcome, I don’t think changing the force can solve the problem. I guess this is not the appropriate reaction coordinate. BTW, if you could solve the issue, please let me know.
Hello, I change the force and the upper sheet can not move to the original position. You can see my US histograms, but the PMF still can not calculate in this way. Have you met this situation?
Thanks a lot.
I’m not sure if you “position restrained” the bottom sheet or top sheet but whatever you did you shouldn’t restrain both of them because then you have no movement in your system and no PMF. What you have to do is restraining all the atoms in one sheet and then defining an umbrella potential between the COM of the two sheets. I recommend defining another reaction coordinate because I couldn’t get any reasonable answer with this reaction coordinate. Not all the reaction coordinates are feasible.
Dear Ehsan, I am very gratefully for your patient answer.
I wonder I have known why I can’t calculate this PMF in this way.
Firstly, I define two groups, which are the edges of the top-layer and the uderlying adjacent layer edge along the z axis. When carrying out the pull code, I freeze the lower layer edge and pull the upper layer edge along the z axis. I set the pull-coord1-k=50000 and pull-coord1-rate=0.001 to get the initial configuration.
Secondly, I get the US windows, whose bin width is 0.05nm.But in this part, I still freeze the lower edge. And the upper edge of the sheet can move within 0.02nm-0.05nm along the z axis(move down). I wonder this setting is the main reason why my calculated PMF is zero.
I would try agin, namely free the lower edge of the sheet and calculate again.
Also, I have try lammps with ABF(the adaptive biasing force) algorithm. It is a hard way to learn and carry out the simulation from zero, but with your advise and kindness, I really feel active. Thank you very much.
It feels like you’re doing it right. your histograms are ok too but it seems there’s something wrong with your PMF calculations. Can you send me all your pull simulations along with umbrella_pullx.xvg and tpr files? Not sure if you can upload it here or not, if not you can reach me at ehsan.shahiny@gmail.com
