From: Ashar Malik (
Date: Fri Dec 15 2017 - 18:56:57 CST

> Is it possible for VMD to calculate the alignment for the entire molecule
> while RMSD is only calculated for the backbone.


I think if a problem exist it has to come from the way you are aligning
A quick check of this would be to load trajectory A into VMD and without
aligning do

set sel [atomselect top all frame 0]
$sel writepdb trajA_0.pdb

Close VMD

Open VMD and load trajectory B and write its frame 0

set sel [atomselect top all frame 0]
$sel writepdb trajB_0.pdb

So now you can compare your reference configuration to trajA_0.pdb and
or even just comparing the two frames trajA_0.pdb and trajB_0.pdb with one
another should return 0.

If the 0 frames are what you say they are - this should return the same
numbers or 0 depending on what you end up comparing.
I don't know how VMD visualizer tool works as I do all of my calculations
with code.
So doing the above will ascertain if your starting frames are identical or

On Sat, Dec 16, 2017 at 11:35 AM, Monika Madhavi <>

> Hi Ashar,
> I did all this analysis using VMD visualizer tool. I loaded my reference
> molecule in the Reference option and then loaded the two trajectories in
> the Molecule option. After selecting one trajectory, I pressed Align button
> first and then RMSD and plotted it. The same thing was done for the second
> molecule. So in my understanding, the calculation must be done as you
> suggested.
> Trajectory - A(RMSD): {0-r, 1A-r, 2A-r, 3A-r, ... }
> Trajectory - B(RMSD): {0-r, 1B-r, 2B-r, 3B-r, ... }
> But my 0-r for two molecules are different even if they start from the
> same initial configuration.
> One point occurred to me is that, I put the atomselection as Backbone in
> the calculation. Is it possible for VMD to calculate the alignment for the
> entire molecule while RMSD is only calculated for the backbone.
> As I don't have my data with me at the moment, I can't tell you the exact
> values of two RMSD's. But they were like 0.3 for one and 0.45 for the other.
> Thank you.
> Best,
> Monika
> On Fri, Dec 15, 2017 at 10:58 PM, Ashar Malik <> wrote:
>> Ok.
>> 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 <>
>> wrote:
>>> 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
>> --
>> Best,
>> /A
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.