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

[marcello cammarata]

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