Marcus Martin

Do you have a copy of that paper or at least a reference for me to look at? I am not familiar with those terms, but I am a bit out of the loop on the literature these days. Marcus

Looking at the pdb files can be deceiving as you have some molecules wrapping periodically through the box so that can make it look like the molecules are outside of the box, when really they are wrapping around to the other side of the box (each molecule has its center of mass in the box, but the atoms may stick out). That picture of the system after 20000 moves does look strange. If you include all the input and output files from the run I have a much better chance of figuring out what is going...

Looking at the pdb files can be deceiving as you have some molecules wrapping periodically through the box so that can make it look like the molecules are outside of the box, when really they are wrapping around to the other side of the box (each molecule has its center of mass in the box, but the atoms may stick out). That picture of the system after 20000 moves does look strange. If you include all the input and output files from the run I have a much better chance of figuring out what is going...

There is not currently an option for cylindrical unit cells. That isn't a shape that can be periodically repeated to fill space so I am not sure how that would work. If you have a reference to something that describes how that unit cell would function I can take a look at it and estimate how much work it would be to implement.

Howdy Jessie, Looks like a constant volume cube of 63 by 63 by 63. What evidence do you have of the x, y, and z values fluctuating? Marcus Marcus G. Martin 88 Martinez Road Edgewood NM 87015-8222 (505) 363 3179 www.photobirder.com towhee.sourceforge.net

Howdy Jessie, I do not see anything that would be changing the box size, especially given this is a grand canonical simulation. Can you include the output from that simulation so I can check to see that the box values are really changing and not just something else related to x,y,z (like maximum translation values)? Marcus On Wednesday, March 22, 2023, Jessie jessie20230322@users.sourceforge.net wrote: Hello everyone, I'm trying to use GCMC to simulate the nitrogen behavior in the bulk phase at 77.4k....

Howdy, They are processed at the same time. If you run a list of 4 jobs on 4 nodes then it is 1 job per node until they are all done. Marcus On Tue, Aug 23, 2022 at 3:21 AM wangqianqian wqq@users.sourceforge.net wrote: Thanks very much! 1. So, I understand that the MPI version of Towhee which reads from an additional file (towhee_parallel) is not able to be processed by multiple processors, right? 2. In fact, the file(towhee_parallel ) is a batch file, when I use the option towhee -p jobfarm to process...

Pretty much the same, maybe a tiny amount more overhead. Using 4 processors to compute a single task is just 3 processors waiting around while the other one runs the simulation. Perhaps slightly slower due to how your machine communicates. Really want to have more (or equal) jobs than processors for jobfarming.