Re: [gmx-users] Temperature Coupling and Coupling-Groups

2010-03-01 Thread Justin A. Lemkul
David van der Spoel wrote: On 3/1/10 5:13 PM, Justin A. Lemkul wrote: shaya...@post.tau.ac.il wrote: Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I

Re: [gmx-users] Temperature Coupling and Coupling-Groups

2010-03-01 Thread David van der Spoel
On 3/1/10 5:13 PM, Justin A. Lemkul wrote: shaya...@post.tau.ac.il wrote: Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I should use. For example, why

Re: [gmx-users] Temperature Coupling and Coupling-Groups

2010-03-01 Thread shayamra
Hi Justin, Thank you very much for your prompt reply. I will make sure to review the aforementioned references. Regards, -Shay Quoting "Justin A. Lemkul" : shaya...@post.tau.ac.il wrote: Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protei

Re: [gmx-users] Temperature Coupling and Coupling-Groups

2010-03-01 Thread Justin A. Lemkul
shaya...@post.tau.ac.il wrote: Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I should use. For example, why not couple the whole system together? I

[gmx-users] Temperature Coupling and Coupling-Groups

2010-03-01 Thread shayamra
Greetings dear Gromacs users, I would like to create a membrane-protein simulations (popc + protein, water, Na Cl ions, using Berendsen thermostat) and I am not sure which coupling-groups I should use. For example, why not couple the whole system together? I do realize that this is a large