[gmx-users] Re: Hexamer problem/ The N and C termini of peptides

[Justin A. Lemkul]

errabah fatima ezzahra wrote:
> I am sorry to be asking you again but do you start with different 
> velocities  by changing the temperature that will lead to change in 
> velocities, i ma new to Gromacs so i dont know where to change he 
> velocities, i checked the  mdp file and i didn't see any velocity
> 

Keep the temperature the same and change gen_seed.

-Justin

> thank you
> 
> Fatima ezzahra
> 
> ------------------------------------------------------------------------
> *De :* Justin A. Lemkul <jalemkul at vt.edu>
> *À :* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Envoyé le :* Jeudi 7 Juillet 2011 14h55
> *Objet :* Re: Re : Re : [gmx-users] Re: Hexamer problem/ The N and C 
> termini of peptides
> 
> 
> 
> errabah fatima ezzahra wrote:
>  > *
>  >
>  > hello
>  > Does anybody knows why The N and C termini of peptides can be 
> neutralized before running simulation of peptides  ?? i read this some 
> where in a research paper , they dont say why but they do that using 
> acetyl amine groops. Probably to evoid the repulsive interactions 
> between the end of the peptides , please correct if i am wrong as my 
> chemistry is not good, my one trimer is  made of 3 peptides that ends 
> with GLU LEU LEU and the other trimer ends with is LEU GLU LEU , should 
> i worry about neutralizing the c and N termini
>  >
> 
> Capping groups can be added to termini using different software 
> programs.  There is no utility in Gromacs to do so.  Once built, choose 
> 'None' for the termini when running pdb2gmx to build a normal peptide 
> bond between the terminal residue(s) and capping group(s).
> 
> Such groups are often added (1) if artificial terminal attraction or 
> repulsion should be avoided or (2) if the modeled peptide is a segment 
> of a longer polypeptide or protein, in which case such integral charges 
> are an incorrect representation of reality.
> 
>  >  Also what the important of running 20 simulations  of the same 6 
> peptides ???. is that to compare the 20 simulation results and see **** 
> which give better simulation sorry if my question are something i should 
> know. i am trying to find how to get six peptides to self assemble to a 
> hexamer  . i will really appreciate your answers.
>  >
> 
> Running multiple simulations of a given configuration (using different 
> starting velocities) gives better sampling.  You can't conclude anything 
> from a single trajectory.  Just as you wouldn't run a single experiment 
> on the bench and call it conclusive, so too is it true of simulations - 
> if you run just one simulation, how do you know you're not seeing the 
> one outlier in the data set?
> 
> -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
> 
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-- 
========================================

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

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