Re: [gmx-users] Alpha-Helix Dipole

Hi David, I tried to use the option -mutot in g_energy, but all I get is the component dipoles. They match what I've got in the file Mtot.xvg from g_dipoles, which is really high (for all the system: water+ polyala helix, fluctuates between 100 and 300 D), but in adip.xvg (the average) the valu

Re: [gmx-users] Alpha-Helix Dipole

[EMAIL PROTECTED] wrote: Just one more thing, David. I read the manual, but I couldn't realize: is the average dipole, (at the top of the g_dipoles output) the overall dipole of the system? (also in the adip.xvg, plotted against time). Because all I want to know is whether the system has a low d

Re: [gmx-users] Alpha-Helix Dipole

Just one more thing, David. I read the manual, but I couldn't realize: is the average dipole, (at the top of the g_dipoles output) the overall dipole of the system? (also in the adip.xvg, plotted against time). Because all I want to know is whether the system has a low dipole moment (which in the

Re: [gmx-users] Alpha-Helix Dipole

Thank you for the guidance, David. Now I got it, but a thing that also helped was to set the option -pbc inbox in trjconv, which I didn't know if I had to (I read the manual, but even so, I didn't know). Now I see the water dipole counterbalances the entire protein one (I was testing in PolyALA,

Re: [gmx-users] Alpha-Helix Dipole

[EMAIL PROTECTED] wrote: Hi David Thank you very much for the reply! So, which group, in the end, shall I select in g_dipoles to see the dipole? And how to use trjconv after editconf the way you told me? (the input/output of editconf is a .gro file and of trjconv is .trr/.xtc files) And whose

Re: [gmx-users] Alpha-Helix Dipole

Hi David Thank you very much for the reply! So, which group, in the end, shall I select in g_dipoles to see the dipole? And how to use trjconv after editconf the way you told me? (the input/output of editconf is a .gro file and of trjconv is .trr/.xtc files) And whose group shall I select in th

Re: [gmx-users] Alpha-Helix Dipole

[EMAIL PROTECTED] wrote: Hello I'm a beginner user of GROMACS, and I'm currently trying to simulate some alpha helices in an explicit water box to extract some initial structures for subsequent quantum mechanical calculations (which uses pbc as well). I'd like to know if there's a way to chec

[gmx-users] Alpha-Helix Dipole

Hello I'm a beginner user of GROMACS, and I'm currently trying to simulate some alpha helices in an explicit water box to extract some initial structures for subsequent quantum mechanical calculations (which uses pbc as well). I'd like to know if there's a way to check if the dipole moment of