[gmx-users] request

[Mark Abraham]

----- Original Message -----
From: leila separdar <separdar.leila at gmail.com>
Date: Sunday, November 21, 2010 19:15
Subject: Re: [gmx-users] request
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


> 
> hi 
> do I need any .pdb file for making .gro and .top file? 
>   
> I make .pdb  file with hyperchem software and then I used pdb2gmx command in order to make .gro and .top files. but I think my way is wrong. is it true?


Sounds OK. We don't have anywhere near enough information to tell. If you'd done some tutorial material and perhaps some simple "normal" GROMACS simulation of your own, you'd have more confidence in your capacity to design a workflow.


Mark


>   
> is there anybody that done this simulation? 
> leila 
>   
>   
>   
> 
>  
> On Sun, Nov 21, 2010 at 11:24 AM, Amit Choubey <kgp.amit at gmail.com> wrote:
> Hi, 


> Define an itp file which has the non-bonded info. Then define a mdp (md parameter file) and also make a structure file (gro). Also you need a topology file (top) which corresponds to the structure file. 
> 

> You will have to do some background work. Manual should be your friend. 
> 

> amit
> 


> On Sat, Nov 20, 2010 at 11:32 PM, leila separdar <separdar.leila at gmail.com> wrote:



> I am beginner with gromacs. I would like to simulate the behavior of glassy materials starting with simple Lennard Jones liquid.

> please advise me as to how to begin. 
> a relevent flowchart or tutorial would be of immerse help 
> thank you very much indeed.> 
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101121/e1ea6236/attachment.html>