[gmx-users] Re: Trajectory and ED - (not old question again)

[Kavyashree M]

Dear Sir,

I tried fitting the proteins of the trajectory in pymol
as mentioned in your (Dr. Tsjerk's) tutorial, but later
I tried using the trjconv -fit rot+trans to fit the proteins
in the trajectory as you had mentioned.

I do not observe this degree of movement in protein
when I view the trajectory along any 1-5 eigen vectors.
This trajectory along any of these eigen vector is very minute
and cannot be compared to that obtained after superposing
the structure in the trajectory. Why is it so?
Please let me know if I am understanding the concept wrong.

Thanking you
With regards
M. Kavyashree


On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M <hmkvsri at gmail.com> wrote:

> Thank you Sir!
>
> With regards
> M. Kavyashree
>
>
> On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:
>
>> trjconv -fit rot+trans
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Jun 23, 2011 8:12 AM, "Kavyashree M" <hmkvsri at gmail.com> wrote:
>>
>> Dear Users,
>>
>> Are there any tool for superposing the trajectory
>> structures form MD. Please correct me if I am asking
>> any illogical question.
>> My previous question was regarding the trjconv output
>> pdb trajectory, is there a way to superpose all these
>> structures?
>>
>> Thank you
>> With regards
>> M. Kavyashree
>>
>> On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>> > > Dear users, > >    I...
>>
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