Re: [gmx-users] Fwd: shift the LJ potential

2017-10-11 Thread Faezeh Pousaneh
I see, thanks Mark, Best regards On Wed, Oct 11, 2017 at 3:46 PM, Mark Abraham wrote: > Hi, > > To reproduce the training data for each forcefield, e.g. some experimental > or other computational result, e.g. the density of argon gas under various > conditions.

Re: [gmx-users] Fwd: shift the LJ potential

2017-10-11 Thread Mark Abraham
Hi, To reproduce the training data for each forcefield, e.g. some experimental or other computational result, e.g. the density of argon gas under various conditions. Details of what and how do vary with the force field, are are documented in its literature, of course. Mark On Wed, Oct 11, 2017

Re: [gmx-users] Fwd: shift the LJ potential

2017-10-11 Thread Faezeh Pousaneh
Apart from my own simulation, I do no understand how the values of C6 and C12 are obtained for each atoms in ''atometypes'' in force fields, could you tell me? Best regards On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett wrote: > > > On Wed, Oct 11, 2017 at 5:06 AM,

Re: [gmx-users] Fwd: shift the LJ potential

2017-10-11 Thread Wes Barnett
On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh wrote: > Thank you Wes and Mark, > > Wes, that is what I am trying to do. However, still have problem. > I do not know how to derive sigma, epsilon (or C6 and C12) for my particle? > How the force fields have obtained C6 and

Re: [gmx-users] Fwd: shift the LJ potential

2017-10-11 Thread Faezeh Pousaneh
Thank you Wes and Mark, Wes, that is what I am trying to do. However, still have problem. I do not know how to derive sigma, epsilon (or C6 and C12) for my particle? How the force fields have obtained C6 and C12 values in their .itp files for each atom? Best regards On Tue, Oct 10, 2017 at

Re: [gmx-users] Fwd: shift the LJ potential

2017-10-10 Thread Wes Barnett
On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh wrote: > Hi Mark > > I have a given function for pseudo hard-sphere potential, which has > different powers than LJ and a constant. I have to insert the constant in > order to properly define the cut-off for my hard spheres. >

[gmx-users] Fwd: shift the LJ potential

2017-10-10 Thread Faezeh Pousaneh
Hi Mark I have a given function for pseudo hard-sphere potential, which has different powers than LJ and a constant. I have to insert the constant in order to properly define the cut-off for my hard spheres. I just realized that I can use "user-specified potential". I guess I can include the