Re: [gmx-users] pressure for ambient water

2010-05-17 Thread Justin A. Lemkul
Amit Choubey wrote: On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu

Re: [gmx-users] pressure for ambient water

2010-05-17 Thread Amit Choubey
On Mon, May 17, 2010 at 6:45 AM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Amit Choubey wrote: On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul

[gmx-users] pressure for ambient water

2010-05-16 Thread Amit Choubey
Hi Everyone, I was doing MD with SPC waters and found something which i am not sure how to explain. I made a box of SPC water of dimension 4x4x4 nm^3 and filled with water using grenbox . I then did a nvt simulation at 300 K for 1 ns . I used berendsen coupling and Reaction - Field for coulomb

Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Justin A. Lemkul
Amit Choubey wrote: Hi Everyone, I was doing MD with SPC waters and found something which i am not sure how to explain. I made a box of SPC water of dimension 4x4x4 nm^3 and filled with water using grenbox . I then did a nvt simulation at 300 K for 1 ns . I used berendsen coupling and

Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Amit Choubey
Hi Justin, Since the density (1 gm/cc) and T (300 K) correspond to ambient condition, should not the equation of state dictate a pressure around 1 atm? thank you amit On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: Hi Everyone, I was doing MD

Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Justin A. Lemkul
Amit Choubey wrote: Hi Justin, Since the density (1 gm/cc) and T (300 K) correspond to ambient condition, should not the equation of state dictate a pressure around 1 atm? If the equation of state involves temperature and pressure, yes. Sounds like you want to be using an NPT ensemble,

Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Amit Choubey
On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: Hi Justin, Since the density (1 gm/cc) and T (300 K) correspond to ambient condition, should not the equation of state dictate a pressure around 1 atm? If the equation of state involves

Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Justin A. Lemkul
Amit Choubey wrote: On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amit Choubey wrote: Hi Justin, Since the density (1 gm/cc) and T (300 K) correspond to ambient condition, should not the equation of state

Re: [gmx-users] pressure for ambient water

2010-05-16 Thread Amit Choubey
On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amit Choubey wrote: On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Amit Choubey wrote: Hi Justin, Since the density (1 gm/cc) and T (300 K)