I really appreciate your thoughts. I know about the words like "exact" or
"correct" does not stand in such scenario. I just needed an expert opinion
regarding the quality assurance of the equilibrated structure. People often
tend to ask question like how can you say that your model is properly
equi
On Tue, 21 Mar 2017 13:09:46 +0530
abhisek Mondal wrote:
> Hi,
>
> I just have a basic query.
>
> I'm working with a protein-ligand system with a goal of performing
> Umbrella sampling in gromacs. So first, after I build the complex, I'm
> going for NVT and followed by NPT equilibration
Hello Mark,
I guess that's an endless question and will vary based on what kind of
ions used in equilibration. So how do I made a decision that I got the
correct equilibrated structure for my production run ? Is it pressure,
density, temperature convergence or I'm missing something?
On Tue, Ma
Hi,
On Tue, Mar 21, 2017 at 8:40 AM abhisek Mondal
wrote:
> Hi,
>
> I just have a basic query.
>
> I'm working with a protein-ligand system with a goal of performing
> Umbrella sampling in gromacs. So first, after I build the complex, I'm
> going for NVT and followed by NPT equilibration
Hi,
I just have a basic query.
I'm working with a protein-ligand system with a goal of performing
Umbrella sampling in gromacs. So first, after I build the complex, I'm
going for NVT and followed by NPT equilibration of 20ns each. After
equilibration, is it mandatory that my equilibrated
