Re: [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

On 8/2/13 10:33 AM, wood irene wrote: Hello thanks for the answer I've tried this option, but the obtained result is the g_potential with the popc profile plotted from 0 to 7nm, being one monolayer from 0 to 3.5, region corresponding to "water" phase at z=3.5 and the other one monolayer from 3.

Re: [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

Hello thanks for the answer I've tried this option, but the obtained result is the g_potential with the popc profile plotted from 0 to 7nm, being one monolayer from 0 to 3.5, region corresponding to "water" phase at z=3.5 and the other one monolayer from 3.5 to 7. In fact lipid bilayer core is at z

Re: [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

On 8/1/13 6:55 PM, wood irene wrote: Hi all I'm trying to calculate the electrostatic potential of POPC membrane systems from a trajectory. When I use g_potential, the calculation is well done but the results are plotted from 0 to 7 nm of Z coordinates, with the bilayer center near to 3.5nm. Is

[gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

Hi all I'm trying to calculate the electrostatic potential of POPC membrane systems from a trajectory. When I use g_potential, the calculation is well done but the results are plotted from 0 to 7 nm of Z coordinates, with the bilayer center near to 3.5nm. Is possible, modifying the trajectory in or

[gmx-users] g_potential

Dear Gromacs users, a)I wish to probe the change in electrostatic potential around a residue/ a group of residues throughout the trajectory. Will the g_potential output be reliable in this regard? b) Is there any way available to probe the change in energy associated with a residue upon the chang

[gmx-users] g_potential

Hi there, I want to have a potential distribution of my box using g_potential, My system includes 7100 particles (anions and cations), when should i apply this command? I mean before or after a mdrun? before or after getting the equilibrium trajectories? should i insert the g_potential command rig

[gmx-users] g_potential calculation method

Dear Gromacs experts How can I find the theoritical method which is employed by Gromacs in order to caculate the electrostatic potential? Here is what is written in manual about g_potential: "The potential is calculated by first summing the charges per slice and then integratingtwice of this cha

Re: [gmx-users] g_potential

minnale wrote: Hi, I have small doubt that when we calculate elctrostaic potenitial of POPC ,get system with neutral, POPC positive and water negative values, what is the reason behind that POPC has positive and water has negative values. I'm not terribly familiar with g_potential, but in

[gmx-users] g_potential

Hi, I have small doubt that when we calculate elctrostaic potenitial of POPC ,get system with neutral, POPC positive and water negative values, what is the reason behind that POPC has positive and water has negative values. water has H+ ion and OH- ion it should be neutral but why negative va

RE: [gmx-users] g_potential problem

Thank you very much, Jochen! Candy> Date: Mon, 17 Dec 2007 09:09:27 +0100> From: [EMAIL PROTECTED]> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] g_potential problem> > CandyCandy wrote:> > Hello!> >> > I am a new beginner of Gromacs. I am trying to

Re: [gmx-users] g_potential problem

CandyCandy wrote: > Hello! > > I am a new beginner of Gromacs. I am trying to use g_potential to > calculate the potential across the membrane. But I only got the 2D > plot (potential vs x axis). Can I get the 3D plot (potential vs x vs > y) by using g_potential? No, you would have to implement thi

[gmx-users] g_potential problem

Hello! I am a new beginner of Gromacs. I am trying to use g_potential to calculate the potential across the membrane. But I only got the 2D plot (potential vs x axis). Can I get the 3D plot (potential vs x vs y) by using g_potential? Thanks in advance for your kind help! Candy

Re: [gmx-users] g_potential: better precision

이 선주 wrote: > Dear All, > > I am trying to calculate membrane potential from the charge density. I > have calculated membrane potential from the charge density profile > obtained from g_potential function. But I've got unmatched potential > between block-averaged(10 ns *6) potential and the pot

[gmx-users] g_potential: better precision

Dear All, I am trying to calculate membrane potential from the charge density. I have calculated membrane potential from the charge density profile obtained from g_potential function. But I've got unmatched potential between block-averaged(10 ns *6) potential and the potential from the whole

Re: [gmx-users] g_potential

mahbubeh zarrabi wrote: Dear user How can I calculate electrostatic potential in md time? what is index file in g_potential? It sounds like you should be doing some reading of the manual. It's really a very good introduction to MD concepts and moves naturally into GROMACS-specifics. Mark __

[gmx-users] g_potential

Dear user How can I calculate electrostatic potential in md time? what is index file in g_potential? thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

[gmx-users] g_potential problem

Dear Gmxers:   In my simulation, I applied a uniform electric field across the whole system, and I used g_potential -f full -s full -o -sl 200 to observe the voltage drop along z direction.   I am confused with the voltage distribution. What time is it referred to? Or, it is an average over