Re: TMD SIMULATION - RMSD DOUBT

From: Semorale (semorale_at_gmail.com)
Date: Wed Jul 09 2008 - 10:30:34 CDT

thanks for your answer, is very helpful.

I am using the NAMD cvs version, which should be corrected the problem of
TMD in the serial version. Hence my doubt about why it is not possible to
reach the final structure.

One more thing. Could do you indicate to me, how to align each frame before
calculating the RMSD in VMD?

Thanks in advance,

2008/7/8 Joshua Adelman <jadelman_at_berkeley.edu>:

> Samuel,
>
> Two things to consider:
> 1. TMD does an alignment of the current structure with the target
> structure, so if in VMD you are doing RMSD without aligning each frame to
> the target frame you're going to get different answers.
> 2. There were some problems with the MPI vs serial version of TMD in NAMD:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5928.html
> I believe the problem was corrected in the CVS version but not the
> distributed executable.
>
> Josh
>
>
>
>
> On Jul 8, 2008, at 6:05 PM, Semorale wrote:
>
> Hi all!!
>>
>> I realize a targeted MD simulation . On having analyzed the results, I
>> find with some "surprises" that I would like to help me to resolve:
>> 1.-On having initiated the simulation, NAMD indicates that the RMSD of TMD
>> simulation is 14, and diminishing (as it must be in TMD). But when I
>> graphical the RMSD of the trayectory in VMD (RMSD trayectory tool), the
>> RMSD:
>> a) It goes in increase
>> b) it never reaches 14, only reaches 4
>>
>> Why the RMSD so different?... At best cases, the graph in VMD should begin
>> in 4 and to reaches to 0, but it is on the contrary.
>>
>> 2.-NAMD indicates that on having finished the simulation (3ns), the RMSD
>> is virtually 0 (0.000103125), which means that it reach the final structure.
>> Nevertheless, on having observed the path, it does not appreciate that the
>> final structure is reached. Why is this? ? Is it a convergence problem of
>> TMD in NAMD? Is simulation very short time?
>>
>> Any suggestion to me is useful.
>> Thanks in advance
>>
>> SAMUEL
>>
>
>
> ------------------------------------------------------------------------------------------------------
> 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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