From: Monika Madhavi (
Date: Fri Dec 15 2017 - 06:30:24 CST

The reference frame I use is a separate pdb file of the same system. I used
the same reference for the calculation of rmsd for both simulations. Given
that the starting configuration of both simulations are same and the
reference is the same, I expected the RMSD plot to start from the same
point. Because my reference is different from the zero time configuration
of both the simulations, neither RMSD values would be zero but I expect
them to be some single value.


On 15 Dec 2017 22:10, "Ashar Malik" <> wrote:

> For simplicity I am going to break this problem down.
> Your starting frame for each of the two trajectories is the same. Lets
> call this *"0"*.
> Then your two trajectories can be represented by:
> Trajectory - A: {0, 1A, 2A, 3A, ... }
> Trajectory - B: {0, 1B, 2B, 3B, ... }
> Lets say that trajectory *"A"* is with the constraints and *"B"* without
> the constraints.
> RMSD is calculated by comparing each frame in a trajectory to a reference
> frame. If you didn't change this, the default should have been frame *"0"
> *which is the starting frame.
> So the following comparisons will have been made.
> Trajectory - 1(RMSD): {0-0, 1A-0, 2A-0, 3A-0, ... }
> Trajectory - 2(RMSD): {0-0, 1B-0, 2B-0, 3B-0, ... }
> If I understand correctly your RMSD plots start at non-zero values. Right?
> Here are some situations.
> 1. Do your plots start at frame 0? If they do it must be a value of 0
> for both plots. In which case the starting values should be identical for
> both plots because frame 0 is compared to itself in both plots.
> 2. Do your plots start at frame 1? In which case why would want them
> to be the same? Frame 1A and 1B are not the same. So why should you expect
> the same RMSD? (This is what is likely happening).
> There may be other reasons - e.g. your trajectory alignment method which
> may also result in a value mismatch, but I think the previous two points
> are important. If you provide more evidence and that doesn't explain the
> difference you can write back and some one will help.
> On Fri, Dec 15, 2017 at 11:55 PM, Monika Madhavi <>
> wrote:
>> Hi all,
>> I minimised and equilibrated a protein water system. Then I used the
>> final configuration of this system to start two simulations with the same
>> parameters except the constraints on backbone atoms. When I calculated the
>> rmsd using Rmsd visualiser tool, the rmsd starts from two values for the
>> two trajectories. I can't figure out what could be the reason for this. Any
>> insight would be appreciated.
>> Thank you
>> Best,
>> Monika
> --
> Best,
> /A