Yes, irest was set to 1.. :(
On Tue, Jan 3, 2017 at 2:15 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Tue, Jan 3, 2017 at 7:09 AM, Elisa Pieri <elisa.pieri90.gmail.com>
> wrote:
> > Actually, I got what happened: I calculated 2 ns pH-REMD with 12
> replicas,
> > from pH 1 to pH 12. Then, due to a reduced available walltime, I decided
> to
> > restrict my calculations to pH range 3-8 for further 20 ns, so I took the
> > cpin newly created by the 2 ns trajectories step as input.
> Unfortunately, I
> > didn't notice that the replicas pH values were 1 2 7 8 10 and 11.
> > But honestly I thought that, since I had specified the pH in the mdin,
> the
> > pH value would be adjusted to values between 3 and 8..
>
> This is only the case when the 'irest' namelist variable is '0', i.e.
> you are *not* restarting a run. Did you have 'irest' set to '1'?
>
> > So what I have now is replicas with pH values equal to 1 2 7 8 10 and 11,
> > right? And..the keyword "solvph" in the mdin is pretty useless, isn't it?
>
> Again, only when 'irest=1'. If you set 'irest=0' the values specified
> in the MD input will be used. Let us know if this is not the case.
>
> -Dan
>
> >
> > On Mon, Jan 2, 2017 at 9:33 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> >
> >> Use the command "ncdump -h" (to get the header information) for each of
> the
> >> trajectories.
> >>
> >> Do they all have the same number of frames?
> >>
> >> Another suggestion is to use the "ensemble" command in cpptraj, which
> will
> >> analyze all replicas in the same run.
> >>
> >> HTH,
> >> Jason
> >>
> >> On Mon, Jan 2, 2017 at 3:31 PM, Elisa Pieri <elisa.pieri90.gmail.com>
> >> wrote:
> >>
> >> > Dear Amber people,
> >> >
> >> > I have 6 pH-REMD .nc trajectory files (from tappo.003 to tappo.008). I
> >> used
> >> > this script (which already worked fine several times with other
> systems):
> >> >
> >> > for ph in 3 4 5 6 7 8
> >> > do
> >> > cat > cpptraj.in << mamihlapinatapai
> >> > parm tappo.parm7
> >> > trajin tappo.003 remdtraj remdtrajtemp ${ph}.00
> >> > autoimage
> >> > trajout tappo_${ph}.pdb
> >> > mamihlapinatapai
> >> > cpptraj tappo.parm7 cpptraj.in
> >> > rm -f cpptraj.in
> >> > done
> >> >
> >> > For some reason, tappo_7.pdb and tappo_8.pdb were perfectly done,
> while
> >> the
> >> > files for the other pH values where empty. If I used cpptraj
> >> interactively,
> >> > this is what I get:
> >> >
> >> > > parm tappo.parm7
> >> > Reading 'tappo.parm7' as Amber Topology
> >> > > trajin tappo.003 remdtraj remdtrajtemp 5.00
> >> > Found 6 replicas.
> >> > Reading 'tappo.003' as Amber NetCDF
> >> > > autoimage
> >> > AUTOIMAGE: To box center based on center of mass, anchor is first
> >> > molecule.
> >> > > trajout tappo_5.pdb
> >> > Writing 'tappo_5.pdb' as PDB
> >> > > go
> >> > ---------- RUN BEGIN ------------------------------
> -------------------
> >> >
> >> > PARAMETER FILES (1 total):
> >> > 0: tappo.parm7, 31941 atoms, 9611 res, box: Trunc. Oct., 9386 mol,
> 9379
> >> > solvent
> >> >
> >> > INPUT TRAJECTORIES (1 total):
> >> > 0: REMD trajectories (6 total), lowest replica 'tappo.003' (reading
> >> 20000
> >> > of 20000)
> >> > Looking for frames at 5.00 K
> >> > Coordinate processing will occur on 20000 frames.
> >> >
> >> > OUTPUT TRAJECTORIES (1 total):
> >> > 'tappo_5.pdb' (20000 frames) is a PDB file
> >> >
> >> > BEGIN TRAJECTORY PROCESSING:
> >> > .....................................................
> >> > ACTION SETUP FOR PARM 'tappo.parm7' (1 actions):
> >> > 0: [autoimage]
> >> > Original box is truncated octahedron, turning on 'familiar'.
> >> > Anchor molecule is 1
> >> > The following molecules are fixed to anchor: 2
> >> > 9384 molecules are mobile.
> >> > Warning: For PDB with MODEL, box coords for first frame only will be
> >> > written to CRYST1.
> >> > Warning: No PDB space group specified.
> >> > ----- tappo.003 (1-20000, 1) -----
> >> > Error: Target replica not found. Check that all replica trajectories
> >> > Error: were found and that the target temperature or indices are
> valid
> >> > Error: for this ensemble.
> >> >
> >> > Read 0 frames and processed 0 frames.
> >> >
> >> > The mdout files do not mention any error. Unfortunately, I'm working
> in
> >> > remote and I don't have the chance to visually check the trajectories
> >> (the
> >> > files are huge). I don't get what is wrong: the .nc files have all the
> >> same
> >> > dimension, so I'm supposing they are fine. Why some pH values are OK
> and
> >> > some others are not? And why cpptraj says "Found 6 replicas." before
> >> > processing and "Target replica not found" after?
> >> >
> >> > Elisa
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> Jason M. Swails
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Tue Jan 03 2017 - 05:30:03 PST
