Re: [AMBER] pre-processing of trajectories

From: <>
Date: Fri, 25 Jun 2010 13:07:30 +0530 (IST)

> On Thu, 24 Jun 2010 12:50:46 +0530 (IST)
> wrote:
>> Thanks a lot for the reply.
>> When I view my trajectories in VMD, the dimeric protein moves to
>> different position within the solvent box but does not come out of
>> the box or the system does not 'break-up'. When I check for
>> equillibrium using standard parameters mentioned in the tutorial such
>> as total enegy, density, temp, etc and also rmsd and radius of
>> gyration, an equilibrium seems to have been reached. However, when I
>> do PCA using ptraj and plot the projections on the top components, it
>> fluctuates rapidly as shown in the figure attached, one reason for
>> which can be the periodic imaging artefact. When I do center and
>> image the plots attached improves and shows equillibration with the
>> projections being distributed around a mean value. But if there is no
>> imaging artefact, why should this happen at all?
> For the purpose of the PCA what you have to make sure is that your dimer
> stays intact at all times. If that is true for all time steps of your
> simulation re-imaging wouldn't have any effect because you RMS fit the
> structure from every frame to the reference structure. Of course, you
> must make sure that your reference is an intact dimer too.
> To check what is happening you could just write out the re-imaged
> trajectory and compare it visually to the original one.
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> AMBER mailing list
hi sir
can u help me out how to plot the projections on the top components of PCA?
i'm new to this analysis


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Received on Fri Jun 25 2010 - 01:00:04 PDT
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