From: Ashar Malik (
Date: Fri Dec 15 2017 - 06:58:29 CST


So this means that the reference is a separate configuration *"r" * which
means we can say the following:

Trajectory - A(RMSD): {0-r, 1A-r, 2A-r, 3A-r, ... }
Trajectory - B(RMSD): {0-r, 1B-r, 2B-r, 3B-r, ... }

And you are saying that 0-r in trajectory A is not the same as 0-r in
trajectory B.

This brings me to the alignment point that I briefly touched earlier.
How do you align your trajectories. Are trajectory A and trajectory B
aligned to their respective frame *"0" *or do you align each trajectory to
an average structure in it or do you align them to this "reference external
structure" you use to compute the RMSD?

reference structure to frame 0 should return the same RMSD value if frame 0
has not moved. If you align each of the separate trajectories to an average
frame within it, then frame 0 would have moved in space and you should not
get the same number between two trajectories.

Also may I ask, what is the RMSD for

your reference configuration and frame 0 of one trajectory
your reference configuration and frame 0 of the other trajectory

On Sat, Dec 16, 2017 at 1:30 AM, Monika Madhavi <>

> 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.
> Best,
> Monika
> 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