Re: question regarding rmsd

From: dhirajks_at_gmail.com
Date: Thu Oct 06 2016 - 17:37:23 CDT

Thank you everyone for your help and suggestions.

Sent from my iPhone

> On Oct 5, 2016, at 3:58 PM, Leandro Martínez <leandromartinez98_at_gmail.com> wrote:
>
>
> Concerning references for RMSD calculations, you might want to take a look
> at this package we developed:
>
> http://leandro.iqm.unicamp.br/mdlovofit/
>
> It computes the RMSD while identifying the most conserved regions within
> the structure, and uses those regions as a reference for the alignment.
>
> It can help to interpret what is actually going on in your simulations if the
> average fluctuations seem to be large.
>
> Leandro.
>
>
>
>
>> On Wed, Oct 5, 2016 at 5:39 PM, Radak, Brian K <bradak_at_anl.gov> wrote:
>> In my opinion, if you want to quantify the fluctuations, you have to be careful in what you choose as your reference for RMSD - looking for anomalous domains, as you have, is probably an excellent idea (and much more informative than simply saying "the RMSD is noisy").
>>
>> Long equilibration times are absolutely acceptable, especially if you are not so sure the initial conditions are physically realistic or relevant. Coming from the nucleic acids community we regularly expect equilibration times > 50 ns - I try to take people at their word when they say a protein system equilibrated faster than that, but it always seems overly fortuitous to me--Apple-Mail-F7540DBA-2FB4-4C62-B87B-A94DBFA38093--

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:45 CST