Hello everyone,
I have an issue with VMD topotool.
In my case, I have a polymeric solution built by moltemplate and everything works well. In this step of simulation, I want to move one polymer chain from one side of the simulation box to another.
Simply I use topo readlammpsdata mysimulation.data full to load my datafile in VMD, then I move the target polymer and I save it by topo writelammpsdata mynewsimulation.data full.
What I get as an output is a totally retyped and re-ordered datafile in atom masses, types, and their coefficients. My coeff data is stored in a separate file and it’s difficult to re-order all the coeffs in this system.
Here is what I load in VMD:
The output of writelammpsdata without any changes in coordinates or topology:
I just wonder if there is something I’m doing wrong or if I’m missing a flag or a keyword.
Thank you in advance,
Saeid