Re: [AMBER] RMSD analysis for cyclo-tetra-peptide

From: Carlos Simmerling <>
Date: Mon, 23 Apr 2012 07:44:56 -0400

- how do you know it is a "problem" and not a property of the peptide?
- rmsd of 0 to 1 (assuming units of angstrom) are not large and indicate
only thermal fluctuations around the same basic conformation
- 3ns is short- have you tried starting from different initial structures,
or using a heating phase? these would help you make sure you are not just
stuck near the initial structure. cyclo peptides can be very rigid and
difficult to sample transitions.

On Mon, Apr 23, 2012 at 7:08 AM, mcj452500 <> wrote:

> Hi, everyone:
> I have used Amber 9 to carry out 3 ns molecular dynamics simulation for
> one cyclo-peptide molcule in water phase to study the conformation
> variation of peptide. In order to find different low energy conformation,
> RMSD values for 3000 conformation extracted from MD trajectory are
> calculated (the initial conformation as the reference). Then RMSD values
> versus time is plotted. It is found that RMSD has a large fluctuation
> between 0 to 1 for cyclo-tetra-peptide and cannot reach the equilibrium.
> But this phenomena is not found for cyclo-tri-peptide and
> cyclo-penta-peptide which RMSD fluctuation is more stable. And extend the
> simulation time has no help to solve the problem.The same settings of MD
> simulations are applied for these systems. Now, I have not found the
> solution to this problem. Anyone can give me some suggestions. Thank you
> for your great help.
> Min Chiju
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Received on Mon Apr 23 2012 - 05:00:03 PDT
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