[gmx-users] Linear CG beads, grompp doesn't work

[XAvier Periole]

I think your original problem is that you define only one charge group for the entire molecule/polymer. You need to define each bead in a separate charge group and things will be fine :)) you do not have charges anyways. 

As far as I know angles have never made martini unstable but the conventional dihedral potential are not suited for martini or any flexible molecule. 

XAvier. 

On Jan 2, 2013, at 4:55, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> On 1/1/13 10:51 PM, Xu Dong Huang wrote:
>> @Justin,
>> 
>> Does the philosophy described in your tutorial apply to CG martini bead models where 1 bead describes the entire CO2 atom? (If I were to do that, assuming)
> 
> Presumably.  As long as you satisfy the criteria mentioned in the tutorial (moment of inertia and total mass), you should be able to get it to work.  I've never dealt with polymers and have very little personal experience with CG models, so I don't know if there are other methodological issues that one might encounter.
> 
> -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
> 
> ========================================
> -- 
> 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