Hi Rahul,
trajin works by "trajin filename [ start stop offset]", according to
the Amber9 manual, p. 246. Trajout works by "trajout filename [
format ]" also from Amber manual.
2000 is the frame number. I save the trajectory file every 0.1 ns, so
frame 2000 would represent 200 ns in the trajectory.
You only want to use a single frame because you are creating a restart
file, so if you are extracting frame 1701, you would use
trajin trajectory.mdcrd 1701 1701 1
trajout restart.rst restart
-Dave
On 3/11/11, Rahul Banerjee <rahul.banerjee.chemistry.msu.edu> wrote:
> Thanks Dave.
>
> But why do you mention "2000" twice in the trajin line? What does it mean?
>
> With best regards,
> Rahul
>
> ________________________________________
> From: david condon [dec986.gmail.com]
> Sent: Friday, March 11, 2011 11:56 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to save a restart file
>
> Hi Rahul,
>
> I have done this many times with pdbs.
>
> You can extract it similarly to the way I do it,
>
> trajin ../mdall.mdcrd 2000 2000 1
> trajout 200ns.wat.pdb pdb
>
> except with "restart" replacing "pdb".
>
> -Dave
>
>
> On 3/11/11, Rahul Banerjee <rahul.banerjee.chemistry.msu.edu> wrote:
>> Dear Amber users,
>>
>> I have a long trajectory for a peptide simulation using Amber. How can I
>> save a particular snapshot (lets say nth snapshot) from the mdcrd file as
>> a
>> restart (rst) file. I want to start another simulation from the new
>> restart
>> file.
>>
>> Thank you for your comments and suggestions.
>>
>> With best regards,
>> Rahul
>>
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>>
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Received on Fri Mar 11 2011 - 09:30:10 PST
