[Chimera-users] MD simulation

Александр Харченко torfp at i.ua
Wed May 6 03:49:37 PDT 2020

Good afternoon, dear Chimera team!

My name is Dr. Pavlo V. Zadorozhnii I am trying to simulate the molecular dynamics of a protein. Started with a simple tripeptide RGD, but I have a number of problems:

1) after starting the energy minimization, the molecular dynamics simulation starts automatically, I can't do it step by step;

2) as soon as the conugate gradient minimazation step is started, the structure of the RGD tripeptide disappears;

3) after the calculation, the structure of the tripeptide does not appear and I can not analyze the data. All graphs and charts are blank.

I used Chimera version 1.14. Print Screen is in the app.

Please help me with the problem I have. 

Sincerely, Dr. Pavlo V. Zadorozhniy.

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