[gmx-users] gmx potential for membrane electrostatic potential

Hi gmx users, I am trying to get the electrostatic potential for a simple DMPC lipid bilayer using the following command - gmx potential -f traj.trr -s topol.tpr - n index.ndx -o potential.xvg -sl 1000 --d z -correct Though the electrostatic potential profile that I obtain is similar to those

[gmx-users] gmx potential

Dear All user,I used gmx potential command to obtained electrostatic potential across the DPPE membrane. I think my finding isn't true because there is a peak at the center of bilayer and in the head group there are two maximum that are small and mild in the head group. what is the cause of

[gmx-users] gmx potential

Dear Justin,I used gmx potential command to obtained electrostatic potential across the DPPE membrane. I think my finding isn't true because there is a peak at the center of bilayer and in the head group there are two maximum that are small and mild in the head group. In the same case for DPPC, 

[gmx-users] gmx potential command

Dear Justin,I used gmx potential command to obtained electrostatic potential across the DPPE membrane. I think my finding isn't true because there is a peak at the center of bilayer and in the head group there are two maximum that are small and mild in the head group. In the same case for DPPC, 

Re: [gmx-users] gmx potential

Hi. Interestingly, I did exactly that compared it with the simulation without an applied field and gmx potential does not seem to be consistent at different times even after a 50ns early "equilibration". I am not at work today, but I will make the output available tomorrow. On Mon, Apr 2, 2018

Re: [gmx-users] gmx potential

Hi, Shouldn't you be comparing the distribution with and without the external field to verify that it has an effect that is physically consistent? Even if there was output from mdrun that said "the applied field was blah blah on step x" that still wouldn't mean anything unless the other output is

Re: [gmx-users] gmx potential

Hi. Can anyone else try to answer my query about using gmx potential? I feel there must be a way to use it to check the potential as applied by external electric field. Shreyas On Thu, Mar 22, 2018 at 5:08 PM, Alex wrote: > Not sure what you mean by "correct." The

Re: [gmx-users] gmx potential

Not sure what you mean by "correct." The "voltage" would be the field, times the box size in the direction of the field. Which is of course fake for a periodic boundary. If you're set on doing e.g. permeation studies that require applying a particular voltage across the box, external fields

Re: [gmx-users] gmx potential

Okay. But then how can one confirm that the correct potential is applied if not by looking at the charge distribution? Shreyas On Thu, Mar 22, 2018, 00:32 Alex wrote: > No, you are exactly right -- it does NOT include the external field > explicitly. The external field

Re: [gmx-users] gmx potential

No, you are exactly right -- it does NOT include the external field explicitly. The external field acts as a magical force here and gmx potential would produce a potential distribution based on the resulting charge distribution. The external field itself, once again, however, does not exist in

Re: [gmx-users] gmx potential

I am confused about which potential it actually calculates. As I understand, the electric field (external) adds a force for each charged particle. This ought to change the ion distribution. If I read the gmx potential documentation right, it uses the distribution of the charges in the box to

Re: [gmx-users] gmx potential

It does exactly what it says it does. Which part is misunderstood? Alex On Wed, Mar 21, 2018 at 3:51 PM, Shreyas Kaptan wrote: > Hi. > > Thanks for the reply! Maybe I misunderstood the tool documentation. So what > does it *really* do? > > On Wed, Mar 21, 2018 at 8:27

Re: [gmx-users] gmx potential

Hi. Thanks for the reply! Maybe I misunderstood the tool documentation. So what does it *really* do? On Wed, Mar 21, 2018 at 8:27 PM, Alex wrote: > Also, here is a message for the authors of the documentation: > > *-[no]spherical*(no) > >Calculate spherical thingie > >

Re: [gmx-users] gmx potential

Also, here is a message for the authors of the documentation: *-[no]spherical*(no) Calculate spherical thingie Come on, guys. :) Alex On 3/21/2018 1:24 PM, Alex wrote: Two things: 1. We cannot see your attachment, upload to a file share. 2. gmx potential does not reveal the actual

Re: [gmx-users] gmx potential

Two things: 1. We cannot see your attachment, upload to a file share. 2. gmx potential does not reveal the actual potential drop due to external electric field itself. What it does instead is described in the utility documentation. Alex On 3/21/2018 12:42 PM, Shreyas Kaptan wrote: Dear

[gmx-users] gmx potential

Dear GMX users, I am trying to use the gmx potential tool to calculate the potential created by applying a constant electric field in the Z-direction. I am using the 2018 gromacs version. The electric field was applied with: electric-field-z = 0.00625 0 0 0; 0.1 V voltage for 160

[gmx-users] gmx potential calculation with one sodium ion at the center of box

Dear Gromacs users, I’m testing a simple system that has one sodium ion to check electric field. (NVE simulation) I used gmx potential- to check electric field. According to gromacs manual 5.0.4 (p.8), ‘the potential of an electronic charge at distance of 1nm equals f ~140 units ~ 1.4V.’

Re: [gmx-users] gmx potential and water

hi Alex, try this paper as a starting point: David van der Spoel and Paul J. van Maaren: The origin of layer structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 (2006) Andre On Thu, Jul 21, 2016 at 11:07 PM, Alex wrote: > Hi all, > > What

[gmx-users] gmx potential and water

Hi all, What we have here is a well-equilibrated, well-behaved, 300 ns long simulation of an aqueous system (tip4p, ~50K atoms) at 300K and a version of gmx_potential.c hacked by one of our very well known members. It allows plotting potential in a all of the slices as functions of simulated