[Chimera-users] MD simulation

[Elaine Meng]

Dear Dr. Pavlo V. Zadorozhniy,

1) you can do it step by step.  In the "Run Parameters" tab, each section has a checkbox.  The "Settings: minimization" section has checkbox next to "Minimize", the "Settings: equilibration" section has a checkbox next to "Equilibrate", the "Settings: production" section has a checkbox next to "Include production phase."  If you only want to minimize, then un-check the ones for equilibration and production.  See attached image:



2,3) unclear exactly what happened but perhaps there was some severe strain or clash that caused the structure to "blow up" when starting conjugate gradient ... I can only suggest doing more steps of steepest descent first and/or changing step sizes,  but I don't have any more specific advice.

Also, if you just want minimization and not any molecular dynamics, there are separate tools for Solvate, Add Ions, and Minimize Structure (all of these are in the menu under Tools... Structure Editing).

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 6, 2020, at 3:49 AM, Александр Харченко <torfp at i.ua> wrote:
> 
> 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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