Recent content by user366312

Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in that file. How can I do that? Sometimes people suggest using the `CONECT` field for that purpose. However, some PDB files do not have this field. Example: 4OSK.pdb (Crystal...

I was analyzing this source code of the Ising model. I found the term "transient state". I also found the term in this text: And, in this text: However, firstly, I am not sure if these texts are related to the C# source code. Secondly, I am not sure if that term is "transient state" or...

What is a "transient" value, result, or state in the Ising model? How do we treat these values during the simulation? Do we discard these values? If so, why?

I dropped out of my 2nd and 3rd MSc. Because of clinical depression issues. > ETA: On re-reading your first post, it's not clear what degree you were pursuing that you did not complete. In Poland. MSC in CS.

PhD program to earn a PhD.

Problem is, I dropped out twice.

In Poland, they will not ask for references. The admission is very straightforward. Only, a supervisor is needed. I don't know about Germany/Austria. But, no, I don't have references to back that up.

I will say that I was working as a freelancer at that time.

As far as I understand: Pruning means deleting something. Enrich means to enhance/increase weight. Now my question is, in the case of the PERM algorithm, Are we deleting some polymers chains? Or, are we deleting some beads in all polymer chains? Are we increasing the weights of some...

I already have an MSc from outside the EU. But, I also have an incomplete CS degree from Poland which I dropped out of. European Ph.D. schools often ask for a CV, not "all the transcript from all the attended programs" as they ask in North America. Therefore, can I skip the information...

I am absolutely new to Polymer simulation. I am trying to understand the simulation by analyzing source code written by others. Can anyone tell me what are the differences between the following three source code in terms of their objectives? Monte-Carlo-simulation-of-polymers...

What does it actually mean by a "cut-off" in this PCASSO algorithm?

I see that the minimum cut-off distance is 6. What is the maximum cut-off distance?

https://pubmed.ncbi.nlm.nih.gov/24995959/ What does it mean by PC in this article?

I need to calculate H-bonds in a specific direction of a C-alpha atom of a protein. And, I need to calculate that from a PDB file. Can anyone give me a general guideline/direction/idea regarding how to do that? N.B. I need to write a python program.