[gmx-users] density profile

Dear all, In order to get density profile of a pure system the box has to get extended in one drection (e.g Z) as we do for surface tension calculations or density profile can be also obtained from the usual box filled up with the molecules without need for empty space in Z Thanks for any

Re: [gmx-users] density profile

On 3/31/13 11:41 AM, Elisabeth wrote: Dear all, In order to get density profile of a pure system the box has to get extended in one drection (e.g Z) as we do for surface tension calculations or density profile can be also obtained from the usual box filled up with the molecules without need

Re: [gmx-users] density profile

Thank Justin. I am interested in the density profile at the solvent-air interface. I wanted to see how density changes with position at different pressures...I have the equilibrated boxes at several pressures obtained from NPT but I am not sure whether running g_density on the current simulations

Re: [gmx-users] density profile

On 3/31/13 12:27 PM, Elisabeth wrote: Thank Justin. I am interested in the density profile at the solvent-air interface. I wanted to see how density changes with position at different pressures...I have the equilibrated boxes at several pressures obtained from NPT but I am not sure whether

Re: [gmx-users] density profile

Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I

Re: [gmx-users] density profile

On 3/31/13 1:12 PM, Elisabeth wrote: Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and

[gmx-users] Density Profile

Hi, I obtained the electron density profile for the solvent in protein membrane simulation, For this I used the following commands: ]$ g_density -f md.xtc -s md.tpr -d z -dens electron -o sol.xvg -ei electrons.dat -symm -n index.ndx Although in md.gro file is seen any water in

[gmx-users] density profile of bilayers

Dear all, I wish to calculate the density profile of a lipid bilayer i.e the electron density and this is how I am using the g_density command: g_density -f final.trr -s final.tpr -ei electrons.dat -o density.xvg -ed -symm where electrons.dat contains # of electrons information for each and

Re: [gmx-users] density profile of bilayers

Hello, priyanka srivastava [EMAIL PROTECTED] wrote: Dear all, I wish to calculate the density profile of a lipid bilayer i.e the electron density and this is how I am using the g_density command: g_density -f final.trr -s final.tpr -ei electrons.dat -o density.xvg -ed -symm where