[gmx-users] Lennard-Jones Parameters

Mon Oct 15 11:54:58 CEST 2012

On 10/15/12 5:45 AM, cuong nguyen wrote:
> Dear,
>
> The top file downloaded from PRODRG did not consist of [atomtypes]. Please
> tell me how can I add and use this function?
>

I see no need to change anything about the L-J parameters.  Is there some reason 
you believe them to be incorrect?  If you modify L-J parameters, you're no 
longer using Gromos96 43a1.  In PRODRG topologies, the charges and charge groups 
certainly need changing, but I have never seen a need to hack the L-J parameters.

-Justin

> Best regards,
>
> Cuong
>
> On 15 October 2012 16:43, Peter C. Lai <pcl at uab.edu> wrote:
>
>> Is there no [atomtypes] section in the top file?
>>
>> On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
>>> Thanks for you email.
>>> I already had the .gro and .top files from PRODRG. Now I want to
>> reproduce
>>> these files following the LJ parameters in a published paper (charge,
>> sigma
>>> and epsilon values). I can change the charge in the top file, yet I do
>> not
>>> know how to change sigma and epsilon values.
>>>
>>> Best regards,
>>>
>>> Cuong
>>>
>>> On 15 October 2012 13:57, Peter C. Lai <pcl at uab.edu> wrote:
>>>
>>>> It's hard to understand your question. What do you mean by "reference
>>>> parameters"? You said you already obtained a .gro and .top from PRODRG,
>>>> which
>>>> uses the gromos 43a1 forcefield to derive the parameters, so if you
>> need
>>>> to change the LJ parameters, edit the top file it gave you.
>>>>
>>>> If you want to reproduce the results of a published paper, you should
>> use
>>>> the
>>>> forcefield and parameters specified in that paper and contact the
>> author(s)
>>>> if more details are needed.
>>>>
>>>> On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
>>>>> Thank you very much for your email, Justin.
>>>>> in case I want to use the reference parameters, which force-field and
>>>> what
>>>>> should I do to get the .gro and .top files for this molecule?
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Cuong
>>>>>
>>>>>
>>>>> On 12 October 2012 21:14, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>>
>>>>>>
>>>>>> On 10/12/12 8:04 AM, cuong nguyen wrote:
>>>>>>
>>>>>>>    Dear Gromacs Users,
>>>>>>>
>>>>>>> I got the .gro and .top files of 1-octanol downloaded from PRODRG
>>>> website.
>>>>>>> Please let me know if I can change charge, epsilon and sigma of
>> the
>>>>>>> molecule as written in a paper? and How to do?
>>>>>>>
>>>>>>>
>>>>>> Atom types from PRODRG rarely, if ever, need changing.  Charges
>> can be
>>>>>> taken first by chemical homology (group-based approach that makes
>>>> Gromos
>>>>>> force fields convenient) and then by calculating the charges
>> yourself.
>>>>   For
>>>>>> 1-octanol, it should be very straightforward to obtain parameters,
>> zero
>>>>>> charges on all the C atoms except for the one in the alocohol, then
>>>>>> standard alcohol charges for the C-O-H.  Whether or not those
>>>> parameters
>>>>>> are sufficiently accurate is up to you to decide, but that's the
>>>> approach
>>>>>> one would take with this particular force field.
>>>>>>
>>>>>> -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<
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>>>>>
>>>>>> ==============================**==========
>>>>>> --
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>>>> --
>>>> ==================================================================
>>>> Peter C. Lai                    | University of Alabama-Birmingham
>>>> Programmer/Analyst              | KAUL 752A
>>>> Genetics, Div. of Research      | 705 South 20th Street
>>>> pcl at uab.edu                     | Birmingham AL 35294-4461
>>>> (205) 690-0808                        |
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>> --
>> ==================================================================
>> Peter C. Lai                    | University of Alabama-Birmingham
>> Programmer/Analyst              | KAUL 752A
>> Genetics, Div. of Research      | 705 South 20th Street
>> pcl at uab.edu                     | Birmingham AL 35294-4461
>> (205) 690-0808                        |
>> ==================================================================
>>
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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

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