Dear Marc van der Kamp
Thanks for your quick reply.
you are right : 2) 200 ps equilibration (NVT).
There is not cpptraj in amber 10 manual.
please explain more.
On 1/25/12, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> Read the AmberTools manual. Ptraj (& cpptraj) can read in trajectory files
> and calculate RMSD.
> Marc
> PS are you not doing NVT in your first equilibration / heating step?
> On 25 Jan 2012 10:45, "Atila Petrosian" <atila.petrosian.gmail.com> wrote:
>
>> Dear amber users
>>
>> I did md simulation of protein as follows:
>>
>> 1) minimization
>>
>> 2) 200 ps equilibration (NPT)
>>
>> 3) 300 ps equilibration (NPT)
>>
>> 4) 1000 ps production run (NPT)
>>
>> In analysis step, I want to obtain RMSD in all of the simulation time
>> (200+300+1000 = 1500 ps)
>>
>> how to do that?
>>
>> any help will highly appreciated.
>>
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>>
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--
Atila Petrosian
Ph.D. student of BioPhysical Chemistry
University of Oulu,Finland
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Received on Wed Jan 25 2012 - 03:30:02 PST
