Re: [gmx-users] coarse grain dynamics

thanks all for the discussion. On Tue, May 25, 2010 at 5:42 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> Thanks for the comments and info, but is there any way to take a >> particular  frame for eg. the last frame  of CG simulation and extend >> the run into all-atom simulation further

Re: [gmx-users] coarse grain dynamics

ram bio wrote: Thanks for the comments and info, but is there any way to take a particular frame for eg. the last frame of CG simulation and extend the run into all-atom simulation further ... There are tools out there to reconstruct an atomistic representation of a CG system (see link be

Re: [gmx-users] coarse grain dynamics

Thanks for the comments and info, but is there any way to take a particular frame for eg. the last frame of CG simulation and extend the run into all-atom simulation further ... On Tue, May 25, 2010 at 5:32 PM, Jared James Thompson wrote: > I agree with Justin on this one. Simulations run using

Re: [gmx-users] coarse grain dynamics

I agree with Justin on this one. Simulations run using CG that is not optimized for reconstruction may not actually reflect the type of interactions you are looking for. The current result of this simulation may not directly correspond to a full atomistic result, so even if a reconstruction were pe

Re: [gmx-users] coarse grain dynamics

ram bio wrote: thanks, but i am using gromacs version 4.0.07 I think the general consensus thus far is you won't be able to do what you want without significant effort to reconstruct your system, and perhaps then you should question whether any tools that seek to build optimal hydrogens f

Re: [gmx-users] coarse grain dynamics

thanks, but i am using gromacs version 4.0.07 On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi wrote: > Hi, > To change between representations (atomistic <--> coarse grained), if you > are using the MARTINI FF, you can use the modified version of Gromacs 3.3, > check here: http://md.

Re: [gmx-users] coarse grain dynamics

Hi, To change between representations (atomistic <--> coarse grained), if you are using the MARTINI FF, you can use the modified version of Gromacs 3.3, check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt If you don't want to switch to full-atomistic representation, check which CG

Re: [gmx-users] coarse grain dynamics

There are programs around for reconstruction of full-atomistic representations from coarse-grained representations, however. I don't know if there are any available for the GROMACS architecture. Quoting Nuno Azoia : > Hi there! > > I never worked with coarse grain simulations, but if you used

Re: [gmx-users] coarse grain dynamics

Hi there! I never worked with coarse grain simulations, but if you used a coarse grain methodology you didn't include all the atoms, so you didn't included hydrogens. So now you can not see them, of course. They are not there. If you need to "know the hydrogen bond interactions" you need to do so

[gmx-users] coarse grain dynamics

Dear Gromacs Users, I have done coarse grain simulation for 2 peptides in bilayer for 1000ns, and now i would like to know the hydrogen bond interactions between these two peptides. Please let me know how to do this, i can visualize the trajectory in VMD, but unable to calculate the hydrogen bondi