Hey y'all,
Ran some additional simulations and, unfortunately, I'm still experiencing
problems. Here's the mdp file that I used:
integrator = md
nsteps = 2000 ; 20 ns
dt = 0.001000
nstlist = 20
ns_type =
On 3/24/20 3:09 AM, Wesley Michaels wrote:
Hi,
Thanks for your reply! I built the topology with my own script, as opposed
to using pdb2gmx. Following Bogdan's instructions here (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html),
I specified all
Hi,
Thanks for your reply! I built the topology with my own script, as opposed
to using pdb2gmx. Following Bogdan's instructions here (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html),
I specified all instances of 1-4 pair interactions (i.e. pairs of atom
Hi
On Sat, Mar 21, 2020 at 3:20 AM Wesley Michaels
wrote:
> Hello,
>
> I hope this message finds you well! I'm running a pretty simple simulation
> of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P =
> 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are
Hello,
I hope this message finds you well! I'm running a pretty simple simulation
of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P =
1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting
large, unstable volume fluctuations when I use the combination of
