[gmx-users] force field parameters

[Justin Lemkul]

Please keep the discussion on the list.

On 9/23/12 11:45 AM, Asaf Farhi wrote:
> Dear Justin
>
> Thank you very much for the reply.
> I apologize that I take of your time.
> I need this file in order to demonstrate a method for free energy calculation that I'm working on (using Matlab).
> I don't have Gromacs installed. If you can, and it's legal I would be happy to have such a file so I can use
>   realistic parameters in the simulation. I haven't found such a list with units and I've spent almost a
> day in total. I will cite the relevant article of course.
>

Gromacs is free to download.  Obtain the source from www.gromacs.org.  You don't 
even need to install it to access any of the files you need.  They are all in 
the /share/top/*.ff subdirectories of the source tree.

-Justin

> Thanks again,
> Best regards,
> Asaf
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: Saturday, September 22, 2012 10:35 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] force field parameters
>
> On 9/22/12 2:13 PM, Asaf Farhi wrote:
>> Dear Justin
>>
>> Thank you very much for the reply.
>> Can you please instruct me how to download the file?
>>
>
> Each force field has an ffbonded.itp when Gromacs is installed.  They are
> located in $GMXLIB/whatever.ff/
>
> -Justin
>
>> Thanks,
>> Best regards,
>> Asaf
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
>> Sent: Saturday, September 22, 2012 3:53 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] force field parameters
>>
>> On 9/22/12 8:48 AM, Asaf Farhi wrote:
>>> Dear Users
>>>
>>> Hi. I'm looking for a a list of bond stretching parameters for the potential 0.5k(r-r_eq)^2 that has units (k and r_eq).
>>> Can anyone help me with that (article will be good)?
>>>
>>
>> All of that information is in the ffbonded.itp file for whatever force field you
>> like.  Citations for all of them are in the manual.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================