Hi,
Yeah that tutorial is woefully out of date - I’m pretty sure it dates back
to when I was a grad student. It should definitely be updated.
Let me know if you have any trouble with the examples I gave you or If you
have any more questions.
-Dan
On Fri, Jun 17, 2022 at 8:30 AM Juliette Newell <
juliette.newell.postgrad.manchester.ac.uk> wrote:
> Hi Dan,
>
> Thank you for getting back to me, the tutorial I have been using is:
>
> https://ambermd.org/tutorials/advanced/tutorial7/index.php
>
> I was changing the ptraj to cpptraj but I will try with the
> ensemble/ensemblesize commands.
>
> Thank you and best wishes,
> Juliette
> ------------------------------
> *From:* Daniel Roe <daniel.r.roe.gmail.com>
> *Sent:* 16 June 2022 13:47
>
> *To:* Juliette Newell <juliette.newell.postgrad.manchester.ac.uk>; AMBER
> Mailing List <amber.ambermd.org>
> *Subject:* Re: [AMBER] Extract trajectories REMD
>
> Hi,
>
> On Thu, Jun 16, 2022 at 6:36 AM Juliette Newell
> <juliette.newell.postgrad.manchester.ac.uk> wrote:
> >
> > Is there a way to modify this to loop over all temperatures and get a
> trajectory per temperature?
> >
> > The tutorial says:
> > ptraj ala10.prmtop <<EOF
> > trajin remd.mdcrd.001 remdtraj remdtrajtemp $T
> > trajout remd.Ttraj.$T
> > go
> > EOF
>
> Which tutorial are you using? If it mentions ptraj it is probably
> pretty old and out of date (and needs updating).
>
> If you want to extract all of the temperature trajectories at once you
> can use the 'ensemble' command. The 'ensemble' command is like 'trajin
> remdtraj' but it sorts and processes all the replicas at once instead
> of a single target replica. So you could do something like:
>
> cpptraj <<EOF
> parm ala10.prmtop
> ensemble remd.mdcrd.001
> rms R1 first .CA out ensemble.rmsd.dat
> trajout remd.nc
> EOF
>
> This will read in the ensemble of MD trajectories of which
> remd.mdcrd.001 is the "lowest", sort by replica (temperature),
> calculate the RMSD of each member of the sorted ensemble and output to
> the file ensemble.rmsd.dat, and write out the sorted ensemble to
> remd.nc.<ext>, where <ext> will be a number corresponding to the
> sorted ensemble (the corresponding temperature will be printed in the
> output from cpptraj).
>
> If the ensemble is large you can use the same input for cpptraj.MPI to
> process the ensemble in parallel (using as many processes as
> replicas). In parallel you can use to 'ensemblesize' command to
> improve the efficiency of setup. So e.g. if you have a 12 member
> ensemble:
>
> mpirun -n 12 cpptraj.MPI <<EOF
> parm ala10.prmtop
> ensemblesize 12
> ensemble remd.mdcrd.001
> rms R1 first .CA out ensemble.rmsd.dat
> trajout remd.nc
> EOF
>
> Note that in parallel cpptraj will write each member to separate data
> files, so you'll get ensemble.rmsd.dat.<ext>.
>
> Hope this helps,
>
> -Dan
>
>
>
> > Which I modified for my system. But this is what gave the error.
> >
> > Thank you,
> > Juliette
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: 15 June 2022 19:27
> > To: Juliette Newell <juliette.newell.postgrad.manchester.ac.uk>; AMBER
> Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] Extract trajectories REMD
> >
> > Hi,
> >
> > On Wed, Jun 15, 2022 at 5:41 AM Juliette Newell via AMBER
> > <amber.ambermd.org> wrote:
> > >
> > > Hi Dan,
> > >
> > > Thank you for getting back to me.
> > >
> > > I have had a look at the cpptraj manual and also the replica exchange
> tutorial on the amber MD website and I am unsure where I am going wrong.
> > >
> > > The example in the manual says :
> > >
> > > trajin rem.001 remdtraj remdtrajtemp 300
> > >
> > > will this loop over all replicas? Or will I have to change the
> temperature at the end.
> >
> > As I said in my earlier response, you specify the "lowest" replica
> > trajectory, and cpptraj automatically searches for the remaining
> > trajectories based on extension. So for example if you have 4
> > temperature REMD trajectories named rem.nc.001, rem.nc.002,
> > rem.nc.003, rem.nc.004 and you want to process frames at a target
> > temperature of 330 K, you would use:
> >
> > trajin rem.nc.001 remdtraj remdtrajtemp 330
> >
> > Any actions or 'trajout' commands will then only be given the frames
> > at 330 K. Does that make sense?
> >
> > -Dan
>
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Received on Thu Aug 04 2022 - 13:31:56 PDT
