I thought using the keyword time would plot RMSD vs time. Maybe this is
what is actually confusing me. This is my trajin file:
trajin ~/Kaiso/MD/K1/Complex1/Analysis/Cluster/K1_complex1_1_10ns.crd.gz
rms first out Kaiso_K1_complex1_RMSD.out time 0.005 :1-127
Secondly, I am just trying to get the ouput files in 1ns increments. I am
looking at running MMPBSA on the system.
Thank you,
Nicole
On Thu, Dec 12, 2013 at 10:30 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> HI
>
> First, I am confused about "run a 1ns simulation for a total of 10ns"
>
> Second, how do you know that shows 50 ns in the rmsd plot? The rmsd plot
> only looks at the frames in the dynamics file, and has no time
> information per se.
>
>
> On 12/12/13 11:28 AM, Nicole Ippolito wrote:
> > Hello,
> >
> > I am trying to run a 1ns simulation for a total of 10ns; however, when I
> > did the RMSD it showed a simulation of 50ns total. I am unsure at this
> > point of what I am doing wrong and am having a hard time understanding
> how
> > the output works. I have looked at the tutorials and the manuals but am
> > still confused. Below is the in file:
> >
> > &cntrl
> > nstlim=1000000, dt=0.001, ntx=5, irest=1, ntpr=1000, ntwx=1000,
> > temp0=300.0, ntt=1, tautp=2.0, ig=-1,
> > ntb=1, ntp=0,
> > ntc=2, ntf=2,
> > cut=12.0, iwrap=1,
> > &end
> > EOF
> >
> >
> > Any explanation would be greatly appreciated.
> >
> > Thank you for your time,
> > Nicole
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
>
> Colonel Allan R. and Margaret G. Crow Term Professor.
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Thu Dec 12 2013 - 09:00:03 PST
