[gmx-users] Micelle Modeling

[Janowicz, Adrianna C.]

Also, I forgot to mention that I need to throw a protein into the mix. How
would I get both the protein and the DPC into the box?




On Tue, July 12, 2011 10:46 am, Justin A. Lemkul wrote:
>
>
> Janowicz, Adrianna C. wrote:
>> Users,
>> I'm trying to start a micelle modeling project & have tried countless
>> approaches to making a DPC micelle. My problems include:
>> -DPC not being recognized when I try to imput it into the [molecules]
>> seciton of the topology file to account for the DPC molecules in the
>> water
>> topology. Otherwise, the molecule #s do not match. (This approach
>> included
>> using a coordinate file for DPC & using the -nmol fuction in genbox to
>> place the DPC molecules into the water).
>>
>> I would appreciate any help. Even if this means taking a totally
>> different
>> approach in getting the DPC molecules into the box.
>>
>
> The best approach would be to:
>
> 1. Create the topology for a single molecule of DPC
> 2. Generate a configuration of the DPC micelle and edit the number of
> molecules
> in the .top appropriately
> 3. Solvate and let genbox add the correct number of water molecules to the
> .top
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>