Re: 1us simulation of 80k atom system -- how much gross structure movement is expected?

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Jul 20 2010 - 07:58:01 CDT

Hi Ian,

Try with VegaZZ
(http://nova.colombo58.unimi.it/cms/index.php?Software_projects:VEGA_ZZ:Download),
there you can define reference frame and calculate rmsd in respect to
this frame.

Branko

On 7/20/2010 4:03 AM, Axel Kohlmeyer wrote:
> On Mon, 2010-07-19 at 21:06 -0400, Ian Stokes-Rees wrote:
>
> hi ian,
>
> [...]
>
>
>>> You should also try to figure out what structural changes are giving
>>> rise to the RMSD changes; clustering analysis would be a good way to
>>> start.
>>>
>> Does VMD provide tools to cluster conformations? I have done a very
>> rudimentary study of the two primary domains with RMSD relative to about
>> half a dozen points (after aligning all frames around the most static
>> domains).
>>
> our group is currently working on that.
> a first minimal implementation is in the current
> VMD development cvs. the implementation is particularly
> optimized for long (many frames) trajectories.
> i'd be happy to help you get started using it
> and giving us feedback.
>
> there also is an external plugin that allows to
> visualize the results from other clustering packages.
>
> http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/cluster/
>
> [...]
>
>
>> I don't understand why the RMSD isn't reported as exactly zero for the
>> reference frame, and it is unfortunate that the built-in plotter can't
>> have the RMSD range fixed, to make successive plots easily comparable.
>>
> like many of the VMD plugins, it is implemented by somebody
> to satisfy a particular personal need and programmed to the
> taste and capability of the author. typically, people writing
> these plugins are not formally trained as programmers, and
> sometimes not even very experienced (everybody has to start
> somewhere). as you already experienced, keeping the status of
> a plugin in sync with the currently available molecules is
> a particularly difficult to program item. several plugins
> have problems with that, and it took my quite some time and
> feedback from users to program it without (apparent) failures
> for the GUI plugins that i have written.
>
> feedback is always appreciate, code even more. in general, it
> is a good idea to look up the original author and make direct
> contact, but for some of the older plugins, that might be difficult.
> people move on quite quickly in our business.
>
> cheers,
> axel.
>
>
>> I can, of course, save the data, import it into another program
>> bit-by-bit, and then plot these with a fixed Y-axis (RMSD, starting from
>> zero), but it would be so much easier if this had the y-axis fixed to
>> start at zero, and the option of auto-scaling the maximum, or fixing the
>> maximum RMSD value.
>>
>> Thanks for your input.
>>
>> Ian
>>
>
>
>
>
> No virus found in this incoming message.
> Checked by AVG - www.avg.com
> Version: 9.0.839 / Virus Database: 271.1.1/3015 - Release Date: 07/19/10 08:36:00
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:06 CST