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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 03 2017 - 05:30:02 PST
