[gmx-users] Re: Spikes in Backbone RMSD

[Justin A. Lemkul]

Amjad Farooq wrote:
> Hello Justin,
> 
> Thank you for your insights into the g_dist command. I am becoming quite 
> an expert on it now!
> 
> I have another question for you and other GROMACS users:
> I am doing MD simulation on  a protein(35aa)-peptide(12aa) complex and I 
> noticed spikes in backbone RMSD roughly half way into my 10-ns 
> trajectory (please see the attached image). The experimentally measured 
> Kd for this protein-peptide complex is around 100uM, so this complex 
> should not be expected to be very stable but what are those spikes? Do 
> they mean anything or is there something wrong with my MD setup? Please 
> shed light.
> 

You haven't properly corrected for periodicity.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

> Thank you all!
> Amjad
> 
>  
> 
> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* Amjad Farooq <amjadfarooq at yahoo.com>; Discussion list for GROMACS 
> users <gmx-users at gromacs.org>
> *Sent:* Thursday, June 30, 2011 1:54 PM
> *Subject:* Re: [gmx-users] Calculate distance between two atoms
> 
> 
> 
> Amjad Farooq wrote:
>  > Hello everyone,
>  >
>  > I would like to calculate distance between two atoms from an MD run. 
> For example, how do I probe changes in distance between CD atom of Pro23 
> and OE1 atom of Glu75 as a function of simulation time.
>  >
>  >  From the manual, I understand that one should use the command g_dist 
> that includes the index.ndx file. My questions are:
>  >
>  > (1) How do I create an index.ndx file for the the above-mentioned 
> pair of atoms?
> 
> Use make_ndx.  Type 'help' at the prompt for examples.  For indices with 
> just one atom each this is not strictly necessary; you can create the 
> necessary groups with a text editor.
> 
>  > (2) What is the exact format of g_dist that should be applied on the 
> command line?
>  >
> 
> Please read g_dist -h.
> 
> -Justin
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> 
> 
> ------------------------------------------------------------------------
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================