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

Johnny Lu johnny.lu128 at gmail.com
Mon Sep 22 15:44:59 CEST 2014

Hi. I noticed mis-spellings in manual of another MD software that persisted
throughout its versions.

Googling for "polyethylene simulation" gave this article as first result:
http://arxiv.org/pdf/1401.4295v1.pdf, which use lammps.
I'm not sure about the availability, accuracy, and computation cost of the
force field that they talk about.

Personally, I guess simulation is like a film or drama. Using the right
setup and looking from the correct angle (like from the front of the stage)
give reasonable results.
Using the wrong setup, or looking from the wrong direction (like from the
side-way of the stage) can give wrong result.

On Mon, Sep 22, 2014 at 8:50 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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
> http://mackerell.umaryland.edu/~jalemkul
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