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

Justin Lemkul jalemkul at vt.edu
Mon Sep 22 14:50:27 CEST 2014

On 9/22/14 8:46 AM, marcello cammarata wrote:
> 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

All the information you need are in the above pages.  You may want to do some 
simple tutorial material on known species before diving into something that 
requires detailed knowledge of Gromacs file formats and topology organization. 
There is basically a how-to at http://www.gromacs.org/Documentation/How-tos/Polymers

> 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.

You'll encounter the same problem in just about every software you use.  If 
you're using a molecule that is unknown to the force field, you're going to have 
to modify force field and/or topology files in some way.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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