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
>>> _______________________________________________
>>> AMBER mailing list
>>> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 12 2013 - 09:00:03 PST
