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 <[email protected]>
*À :* Discussion list for GROMACS users <[email protected]>
*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 <[email protected] <mailto:[email protected]>>
> *À :* Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
> *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
========================================
-- gmx-users mailing list [email protected]
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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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