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 some gen_seed = -1
and that to generate random seed is that correct ??
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.
Thank you so much
fatima ezahra
________________________________
De : Justin A. Lemkul <jalem...@vt.edu>
À : Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu>
> *À :* Discussion list for GROMACS users <gmx-users@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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