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

errabah fatima ezzahra errabahf at yahoo.fr
Thu Jul 7 21:44:07 CEST 2011

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 

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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