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

Wed Sep 24 02:00:22 CEST 2014

The first couple of responses you received to your question provided the resources in order to do what you are looking to do, and answered the exact questions you have asked here.  Go back and have a look at those and follow the links provided.  They are written in general terms though, since they are written for everyone, not for something as specific as what you are trying to do.

It is important to note that what you are looking to do is not easy, especially for someone that is new to MD and a software package.  If you want to get something out that is useful and not a waste of your time, I would suggest you find someone in the know to collaborate with.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> marcello cammarata
> Sent: Wednesday, 24 September 2014 9:43 AM
> To: Johnny Lu; gmx-users at gromacs.org
> Subject: Re: [gmx-users] I: How to rolled up a polymer chain
> 
> Do you know how change force field?
> how i can do this?
> so the goal can be this, i can consider two molecules asmetilene or
> ethilene or butene, and i want kwon by appling a set of force field the
> mutual distance beetween the two groups.
> 
> How i can do this?
> how is possible to set force field?
> 
> bests
> 
> 
> 
> MARCELLO CAMMARATA
> Ing., Ph.D.,
> 
>  3208790796
> 
> 
> Il Mercoledì 24 Settembre 2014 0:41, Johnny Lu <johnny.lu128 at gmail.com>
> ha scritto:
> 
> 
> 
> 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
> >> --
> >> Gromacs Users mailing list
> >>
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> >
> >--
> >Mohd Farid Ismail
> >mohd.farid.ismail at yandex.com
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
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> posting!
> >
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