[gmx-users] Using tables to construct a z-dependent 12-3 potential

2011-11-26 Thread Olivia Waring
Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would be greatly appreciated. Thank you! Olivia --

Re: [gmx-users] Using tables to construct a z-dependent 12-3 potential

2011-11-26 Thread David van der Spoel
On 2011-11-26 15:58, Olivia Waring wrote: Hello all, I'm wondering if it's possible to use tables to simulate a z-dependent 12-3 potential. I'd have the following function: V(z) = C12/(z-z0)^12 - C3/(z-z0)^3 and I'm trying to construct a table to match. Any hints to get me started would be

Re: [gmx-users] Using tables to construct a z-dependent 12-3 potential

2011-11-26 Thread Olivia Waring
Thanks David! That helped a lot. I'm now trying to use the walls feature with a user-defined potential. My mdp file is shown below: title = Alkanethiol SAM MD ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps,

Re: [gmx-users] Using tables to construct a z-dependent 12-3 potential

2011-11-26 Thread David van der Spoel
On 2011-11-26 21:01, Olivia Waring wrote: Thanks David! That helped a lot. I'm now trying to use the walls feature with a user-defined potential. My mdp file is shown below: title = Alkanethiol SAM MD ; Run parameters integrator = md; leap-frog integrator nsteps