[gmx-users] electrostatic potential

[delara aghaie]

Hello all
I had simulated Tip4p-2005 water system with different concentrations of MgCl2 and Cacl2 salts. I have calculated the Surface tensions of the systems and I see that presence of the salt increases the S.T of water layer.
Now to do more analysis i want to calculate the contributions of water and ions to the electrostatic potential .
I should use g_potential command.
 
I need an index file. Do I need to specify water, Mg and Cl groups in the index file?
is this command format corect?
 
g_potential -f traj.trr -n index.ndx -s topol.tpr ?
 
Please let me know if I should consider anything else?
thanks
Regards
D.Aghaie

--- On Fri, 5/13/11, Justin A. Lemkul <jalemkul at vt.edu> wrote:


From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] pressure in NPT and NVT
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Friday, May 13, 2011, 5:36 PM




Nilesh Dhumal wrote:
> Hello,
> 
> I am using NPT simulation for water - spce model (opls-aa force field).
> I have the reference pressure set at ref_p = 1.0 bar.
> I checked the average pressure using g_energy and it is 2.81972 bar.
> 
> Why there increase in pressure?
> 
> 

Probably the system is not yet equilibrated.

> 
> For NVT simulatin I get the value around average pressure 710.685 bar.
> 
> I am running the simulation at 295 k and  average temp. is 294.98 K which
> look ok.
> 
> 
> Can you tell why there is increase in pressure for NPT and  why there is
> so high value of pressure in NVT.
> 

Because the box is fixed.  It cannot respond to internal forces in your system.  Pressure values during NVT don't mean much.

-Justin

> I am using gromacs version 4.0.7.
> 
> Thanks
> 
> Nilesh
> 

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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