Re: TMD RMSD problem

From: Elif Ozkirimli (ozkiriml_at_gmail.com)
Date: Thu Apr 09 2009 - 11:24:21 CDT

Thanks for the responses.
I am aligning all frames in the dcd before I calculate the RMSD. The
indexing of the atoms is also correct and the same in VMD and NAMD.

I forgot to mention: the RMSD in the NAMD output never falls below 2 (the
RMSDref does fall to 0) but when you wach the simulation in VMD it's obvious
that the TMD is complete and the protein has assumed the target conf.

Elif.

On Wed, Apr 8, 2009 at 11:35 PM, Joshua Adelman <jadelman_at_berkeley.edu>wrote:

> Are you aligning all of the frames in your trajectory before you calculate
> the RMSD? If not the results will surely be different since namd performs
> the alignment when it calculates the tmd force and outputs the rmsd
> Josh
>
>
> On Apr 8, 2009, at 1:21 PM, Elif Ozkirimli wrote:
>
> Dear all,
>
> I am trying to use TMD to move a protein from one conformation to the
> other. I read the initial coordinates and then the target coordinates are
> read within the TMD section with the correct occupancy values. RMSD values
> are reported in the NAMD output file. I then try to calculate RMSD vs time
> for the same coordinate set using VMD. However, the RMSD values in the NAMD
> output file and those I calculate from VMD are different. Does anybody else
> have the same problem?
>
> I had poster earlier about this problem. I was hoping 2.7 would fix this
> but alas it does not.
> Any help or suggestions would be greatly appreciated.
>
> Elif.
>
>
>
> ------------------------------------------------------------------------------------------------------
> Joshua L. Adelman
> Biophysics Graduate Group Lab: 510.643.2159
> 218 Wellman Hall Fax: 510.642.7428
> University of California, Berkeley
> http://nature.berkeley.edu/~jadelman
> Berkeley, CA 94720 USA jadelman_at_berkeley.edu
>
> ------------------------------------------------------------------------------------------------------
>
>
>

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