[gmx-users] ffgmx:diffusion of oxygen

Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such simulations for

Re: [gmx-users] ffgmx:diffusion of oxygen

Sunil Thapa wrote: Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns. But my system is very small 1oxygen molecule in 255 molecules of water. I want to calculate the self diffusion coefficient of oxygen . What I have found that people do such

RE: [gmx-users] ffgmx:diffusion of oxygen

-boun...@gromacs.org] On Behalf Of Sunil Thapa Sent: Tuesday, 28 April 2009 5:40 PM To: gmx-users@gromacs.org Subject: [gmx-users] ffgmx:diffusion of oxygen Respectable Experts Thank you very much David. Yes the msd curve tries to improve if I run for 100ns

[gmx-users] ffgmx:diffusion of oxygen

Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which matches with that given in the gromacs manual. After equilibrating my system of 1 oxygen and 255 water molecules

Re: [gmx-users] ffgmx:diffusion of oxygen

Sunil Thapa wrote: Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 which matches with that given in the gromacs manual. After equilibrating my system of 1 oxygen and

Re: [gmx-users] ffgmx:diffusion of oxygen

Could it be that you have not removed the jumps due to the periodic boudary conditions before using g_msd? Try trjconv -pbc nojump Jochen Sunil Thapa wrote: Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule. And yes it gives

Re: [gmx-users] ffgmx:diffusion of oxygen

Jochen Hub wrote: Could it be that you have not removed the jumps due to the periodic boudary conditions before using g_msd? Try trjconv -pbc nojump Jochen Sunil Thapa wrote: Respectable Justin/David/Mark I used ffgmx force field thinking it as suitable for bonds in the oxygen molecule.