[gmx-users] I: How to rolled up a polymer chain

[Johnny Lu]

Molecular dynamics software, like gromacs, use a set of rules to simulate
the real world.
This set of rules is a force-field.

Force field is the simplified physical rules of the real world that are
hopefully approximately right.
Such simplified rules usually can not describe everything in the real
world.
Usually people have to extend the forcefield by finding the correct
parameters (using spectrums from experiments, quantum mechanical
calculation... just the way that people used to make a force field in the
first place) to simulate drugs within proteins.

You can either extend the force field; so that the force-field describe
polyethylene.
Or use an existing force field that can describe polyethylene.

So far, I guess the force-fields implemented in gromacs can not describe
polyethylene (unless you change the force-fields).

On Tue, Sep 23, 2014 at 2:15 PM, marcello cammarata <mstaxmarcello at yahoo.it>
wrote:

> yes,
>
> i need yto know how it go to tangled, related with the lenght of chain,
> the number of chains in volume unit.
> For now the problem is that when i run pdd2gmx, i don't choose any
> solvent, because there isn't eny solvent, i choose only a kind of force
> field present in the database software. but each time it ask me for the LIG.
>
> I have a bdp file with the chain, made by me.
>
>
>
> MARCELLO CAMMARATA
> Ing., Ph.D.,
>
>  3208790796
>
>
> Il Martedì 23 Settembre 2014 18:25, Mohd Farid Ismail <
> mohd.farid.ismail at yandex.com> ha scritto:
>
>
>
> Can I ask you something.  What do you mean by "rolled up"?  Do you mean
> create the tangled conformation of polymer chains?
>
> --Farid
>
>
> 22.09.2014, 20:46, "marcello cammarata" <mstaxmarcello at yahoo.it>:
> > Hi,
> >  i had checked all the archives, i have read about 100posts in the last
> 2 month.
> > Nobody have problem similar to mine.
> > Problem for me are Two.
> > 1- instead i am a doctor, i am not able to find the right advice at your
> site.
> > 2- In your site there is no space for begginer user.
> >
> > The main pages where i checked are:
> > Residue
> > Chain
> > Polyethylene (PE) simulations in Gromacs - please!
> > .rtp File
> > Force Fields
> > Adding a Residue to a Force Field
> > Modifying a force field
> >
> > But i don't have find any suggestion for my problem.
> > Is there an other blog, that i can't see.
> > i have several of problem with Gromacs,
> > - in Cygwin it doen't work, i got a "bash" comand
> > - the topology need a lig parameters.
> >
> > one more time, below there is my post. I wpould like if you can help me
> to solve this question, instead i can try to use an othere MD software.
> >
> > MARCELLO CAMMARATA
> > Ing., Ph.D.,
> >
> >  3208790796
> >
> > Il Lunedì 22 Settembre 2014 14:20, marcello cammarata <
> mstaxmarcello at yahoo.it> ha scritto:
> >
> > My goal, for now, is to model a polimer (nylon-6) chain, and to find the
> equilibrium position of the chain considering the capacity to be rolled up
> itself.
> > I had create a pdb file using Avogadro software, but when i go to
> gromacs to input the
> >  data using the function pdb2gmx And indipendently of the force field
> that i
> >                           choose i get :that "Residue LIG not found".
> >
> > How to solve this?
> > thanks
> >
> > MARCELLO CAMMARATA
> > Ing., Ph.D.,
> >
> > 3208790796
> > --
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> --
> Mohd Farid Ismail
> mohd.farid.ismail at yandex.com
> --
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