Hi,
Just to expand on trajectory conversion, say your runs are in
subdirectories run1 to run5 and your replica trajectories are named
rem.x.000 etc, and your lowest temperature is 300 degrees. In order to
create the overall ensemble at 300:
trajin run1/rem.x.000 remdtraj remdtrajtemp 300
trajin run2/rem.x.000 remdtraj remdtrajtemp 300
trajin run3/rem.x.000 remdtraj remdtrajtemp 300
trajin run4/rem.x.000 remdtraj remdtrajtemp 300
trajin run5/rem.x.000 remdtraj remdtrajtemp 300
trajout rem.300.nc netcdf
Note that with cpptraj you can also create all temperature
trajectories in one shot, so if you plan on doing a lot of processing
at different temperatures you can create the temperature ensemble in
each subdirectory:
trajin rem.x.000 remdtraj remdtrajtemp 300 remdout temperature netcdf
This will create files 'temperature.<T>', where <T> is the temperature
of that trajectory. You could then create the overall ensemble at any
temperature in a second step:
trajin run1/temperature.300.00
trajin run2/temperature.300.00
trajin run3/temperature.300.00
trajin run4/temperature.300.00
trajin run5/temperature.300.00
trajout rem.300.nc netcdf
-Dan
On Wed, May 9, 2012 at 7:56 AM, Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
> you'll need to write a script if you want to process information from
> multiple log files.
> the structure ensembles can be obtained from ptraj- just use multiple
> traijin lines.
>
> On Tue, May 8, 2012 at 6:43 PM, Nadeem Ahmad Vellore <
> Nadeem.Vellore.utah.edu> wrote:
>
>> Dear AMBER Developers,
>>
>> I need a clarification regarding REMD simulation using AMBER12. I don't
>> want to use the -A option for restarting my REMD simulation (this would
>> make my files too big by appending the data) and hence I used the -O option
>> and divided the simulation into chucks and saved the useful files into
>> respective time-framed directories every specified REMD exchanges.
>>
>> Assuming, I simulated for 5ns with 1ns increment and copied the files in 5
>> different directories. How can I combine the trajectory to find the right
>> exchange probabilities and low temperature ensemble. Since rem.log will
>> start from the begining and forget the information about the previous
>> exchanges.
>>
>> Any idea/comment or hint would be highly appreciated.
>>
>>
>> Regard
>> Nadeem
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>>
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Received on Wed May 09 2012 - 05:30:03 PDT
