[gmx-users] On Decane coordinate file

[Justin Lemkul]

On 5/21/13 1:44 PM, Bao Kai wrote:
> Hi, Rejesh,
>
> Thanks for the reply.
>
> Unfortunately, they does not have the topology file for decane.
>

For a simple molecule like decane, g_x2top can probably create a reasonable 
topology for you.

-Justin

> virtualchemistry.org has some topology files for many organic liquids.
>
>
> Regards
> Rajesh
>
> On Tue, May 21, 2013 at 1:21 PM, Bao Kai <paeanball at gmail.com> wrote:
>
>> Hi,
>>
>> Thank you for your response.
>>
>> I guess I took the problem wrong.  I guess I need a topology file for
>> decane.
>>
>> I did some google search, generally people told that it can be done
>> manually, while this is really not my field.  My field is CFD, while
>> my boss gave me some molecular simulation things to do.
>>
>> I am wondering if there is some more convenient way to generate the
>> the decane topology file.
>>
>> I found some .pdb file, while I failed to generate the .top file with
>> pdb2gmx. Generally the residue name is not correct.
>>
>> I wonder if there is anyone have done this before and would like to
>> provide one .top or .itp file on decane.  Generally any forcefield
>> will work while OPLS-AA forcefield will be better.
>>
>> Thank you very much.
>>
>> Best Regards,
>> Kai
>>>
>>>
>>> On 4/16/13 6:51 AM, Bao Kai wrote:
>>>> Dear all,
>>>>
>>>> I am trying to do some two phase simulations with Decane molecules and
>>>> some
>>>> other smaller molecules.
>>>>
>>>> When I did simulations with smaller molecules, I specifies the
>> properties
>>>> based on each atom, while I just realized it is really not desirable to
>>>> do
>>>> it with Decane molecules ( 34 atoms each molecule).
>>>>
>>>> I am wondering if anyone could provide one coordinate file and the itp (
>>>> or
>>>> .top ) file for the Decane simulation if you have ever done it before.
>>   I
>>>> did not find very detailed Decane molecule models.
>>>>
>>>
>>> You should probably mention what force field you're trying to work with.
>>> For a
>>> simple alkane like decane, writing the necessary .rtp and .hdb (if
>>> necessary)
>>> entries is fairly trivial.  Then just let pdb2gmx do all the work
>> assembling
>>> the
>>> whole topology.
>>>
>>> -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

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