Dear users,<br><br>I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and the following parameters (only a few are given):<br><br>; RUN CONTROL PARAMETERS<br>integrator = md<br>tinit = 0<br>
dt = 0.002<br>nsteps = 125000<br>comm-mode = Linear<br>nstcomm = 1<br><br>nstlist = 10<br>ns-type = Grid<br>pbc = xyz<br>
rlist = 1.0<br>domain-decomposition = no<br><br>coulombtype = PME<br>rcoulomb-switch = 0<br>rcoulomb = 1.0<br>epsilon-r = 1<br>vdw-type = Cut-off<br>
rvdw-switch = 0<br>rvdw = 1.0<br><br>I recently noticed from the manual that the nstlist should be 5 with gromos 96 ff. I have a couple of questions. <br>1. should this be 5 with a 0.001 timestep or with a 0.002 timestep<br>
2. As I have done a lot of work using these parameters I was really looking for some suggestions/advice as to whether I can use any of my data - I;m really clinging onto hope here! And as to how 'badly' this choice/mistake will have affected my work.<br>
<br>Thanks,<br>Les<br>