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

[Justin A. Lemkul]

errabah fatima ezzahra wrote:
> Thank you so much for your help , my pdb file says that gen_seed = 
> 473529 so i will change it to different numbers , but i saw online that  

Your .mdp file, you mean?

> some gen_seed = -1 and that to generate random seed is that correct ??

Yes, with -1 you will get a random number based on the process ID.

> also please  how i can control the starting initial states so that i can 
> have starting from more one initial states??  tried looking it up on 
> line but did not find that much information.
>  

If you generate different velocities, then that is a different state.  If you 
want to control what the velocities are (to some degree), then set gen_seed 
explicitly.  If you want to start from a different configuration, build a new 
starting structure.

-Justin

> Thank you so much
> 
> fatima ezahra
> 
> 
> 
> ------------------------------------------------------------------------
> *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 15h55
> *Objet :* Re: Re : Re : Re : [gmx-users] Re: Hexamer problem/ The N and 
> C termini of peptides
> 
> 
> 
> 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 <mailto:jalemkul at vt.edu>>
>  > *À :* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto: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
> 
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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

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