Great thank you so much for your help! I see the correlation now.
Nicole
On Thu, Dec 12, 2013 at 10:48 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> ok
>
> in the input you had
>
> nstlim=1000000, dt=0.001, ntx=5, irest=1, ntpr=1000, ntwx=1000,
>
> This means run 1M steps with dt=1 fs, for a total of 1 ns, and save
> coordinates every 1000 steps, meaning 1 ps.
>
> Now, when you run ptraj/cpptraj, you set time = 0.005
>
> Why ?
>
> That is what happening, you inputted the wrong value of time there.
>
>
> On 12/12/13 11:44 AM, Nicole Ippolito wrote:
> > 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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> >> --
> >> 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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> >>
> > _______________________________________________
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>
> --
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Dec 12 2013 - 09:00:04 PST
