[Chimera-users] how to generate different starting points to do md simulations

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 22 08:55:20 PDT 2021

Hi Surya,
If you're asking whether there is a way in Chimera, the answer is not really, other than manually rotating bonds yourself.  For some nonbiased approach, you would need to use some other program to generate the starting conformations.  Also keep in mind that Chimera is not recommended for long MD because it is slow compared to other programs, and it does not have many options like replica exchange.

Chimera MD limitations are discussed in earlier posts, including:

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

> On Mar 22, 2021, at 12:00 AM, Seera Suryanarayana <palusoori at gmail.com> wrote:
> Dear chimera users,
> I have a small peptide of 20 residue length and I would like to do the simulations of this peptide at different starting points. How could one can generate the different starting points?  Can I use the replica exchange MD simulations to generate the different starting points? I request you to please suggest me how to generate different starting points of peptide.
> Thanks in advance
> Surya
> Graduate student
> India.

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