jhenin / qwrap Goto Github PK

I really have a problem, which does not let me sleep. During the diffusion process (where I want to observe the input of an ion to a channel), I have been using the wrapAll and wrapWater on options in the config file, at the end of the simulation I have been able to see that there is really the input of ions, but Many authors say that you have to "unwrap" the trajectory, when doing diffusion analysis, then, I have done it, using pbc both only for the ions and for the whole system and in both cases it is not seen that the ion penetrates, so I thought about extending the dynamics, but what happens is that when I extend the dynamics, the structure with which I start is the one that is inside the channel, so all this causes me enormous confusion.
Please, could you tell me in which cases wrapAll or wrapWater can be used in a dynamic.

Dear Prof Hénin,

I have a question about qwrap. Is this suitable for membrane proteins? because this is a rectangular box.

Geo.

I'm try compile on my mac, but it not work

I would like to use qwrap, but I need to perform my calculations on a supercomputer. I do not have administrative access on the supercomputer. I see that it says in the documentation that qwrap can be used without installation by using the command load path_to/qwrap.so. However, I have downloaded the repository and do not see a qwrap.so file. How can I create or find this file to be able to use qwrap on a supercomputer? Would I create this file on my personal computer and then transfer it so the supercomputer? I use a Windows computer but the supercomputer is linux based.

And do not try to wrap or unwrap. Ideally, fall back to PbcTools, or offer the option.