[gmx-users] mdrun with append option
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 1 19:04:06 CET 2011
Sai Pooja wrote:
> I am doing a manual replica exchange(generalized hamiltonian rem) after
> every mdrun. If the replica exchange is successful, then I "exchange
> checkpoint files". For example, consider the following:
>
> Simulation parameters:....................B1.........B2
> Replicas(coordinates and velocities):.R1.........R2
>
> 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY)
> 1. Mdrun run - 500 steps = 1ps
> 2. Attempt exchange - NOT SUCCESSFUL
> 3. Exchange implementation: SKIP
> 4.Continue to next step
>
> .....
> 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY)
> 1. Mdrun run - 500 steps = 1ps
> 2. Attempt exchange - If successful, exchange
> 3. Exchange Implemented by - exchanging checkpointing files
> 4. Continue to next step
>
> 0. Tpbconv to extend simulation time ( using -s, -o and -nsteps ONLY)
> 1. Mdrun with exchanged .cpt files -NOW this is where the problem shows..
> i) The log, xtc files are not appended when beginning after a step
> with a successful exchange attempt:/According to Mark's previous mail,
> this could be a result of mismatch in ensembles. Which means that the
> .cpt is ignored - implying that the mdrun in B1 DOES NOT start from R2./
>
Sounds like a reasonable conclusion.
> Therefore, to make R1 run in B2 and R2 run in B1, do I need to supply
> .cpt to tpbconv instead of mdrun after a successful exchange step?
>
Either tpbconv or grompp can do this. Check the resulting .tpr with gmxdump to
make sure it's using the proper coordinates, velocities, etc from the .cpt file
and you'll have your answer as to whether or not it's working as you want.
-Justin
> To summarize:
> APPENDING HAS NOW BECOME A SECONDARY CONCERN, WHAT I AM INTERESTED IN IS
> A SUCCESSFUL MANUAL REPLICA EXCHANGE RUN AS POINTED OUT ABOVE.
>
> I hope my dilemma is clear now.
>
> Pooja
>
>
> On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Sai Pooja wrote:
>
> From the website:
> "If you change the integrator or ensemble, you should pass the
> checkpoint file to tpbconv only, not to mdrun, since the state
> might change and thus output files can not be appended."
>
>
>
> Are you changing the integrator, ensemble, and/or other settings?
> If not, this statement does not apply. For a simple -append after
> extending via tpbconv, this is not applicable.
>
>
> So now instead of supplying the checkpoint file to mdrun I
> supply it to tpbconv... does this assure that the simulations
> start from the coordinates/velocities specified by the .cpt file?
>
>
>
> For a simple extension, you do not pass the .cpt file to tpbconv.
>
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4
>
>
>
> Thanks Mark. So if the simulation doesn't start from the
> checkpoint
> file, from where are the initial coordinates velocities etc.
> taken
> from?... the trajectory files?
>
>
> Mark's previous message already answered this.
>
> -Justin
>
> Also, I could not find the environment variable... and I
> am not sure
> how to use one.
> Pooja
> On Tue, Feb 1, 2011 at 3:03 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>> wrote:
>
> On 1/02/2011 7:50 AM, Sai Pooja wrote:
>
> I think I have figured out the reason. It is because I am
> carrying out replica exchange (manual) after every
> mdrun. If
> the exchange occurs, I exchange the checkpoint files,
> extend
> the simulation by 500 steps and continue. The new
> simulation
> starts from exchanged cptfile. It seems that whenever the
> exchange occurs, the earlier log,traj files are not
> appended.
> They are instead overwritten. the obv solution is to
> save and
> index these files with the relevant replicas everytime an
> exchange occurs.
>
>
> This would have been good to know earlier. If
> replica-exchange
> leads to the ensemble of the .tpr not matching the
> ensemble of
> the .cpt, then IIRC 4.5.3 mdrun will refuse to start from the
> .cpt, which means the subsequent mdrun will start from
> the .tpr
> only. Certainly a non-appending mdrun prints a warning (or
> error, I forget which) message to the log file, but
> perhaps the
> use of -append (erroneously) doesn't do that. Please have
> a look
> and see if that is the issue. There is an environment
> variable
> that can be set to tell mdrun that you (think you) know
> what you
> are doing mismatching .tpr and .cpt.
>
> Mark
>
>
> However, i have a more general question. Since mdrun
> still
> runs with the exchanged checkpoint files and starts
> from the
> point where the previous run ended, can I be assured
> that an
> exchange has been affected - since tpr files
> correspond to the
> "replica-box" and cpi to the most recent exchanged
> replicas?
> Pooja
>
> On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja
> <saipooja at gmail.com <mailto:saipooja at gmail.com>
> <mailto:saipooja at gmail.com
> <mailto:saipooja at gmail.com>>> wrote:
>
>
> I manually index checkpoint files after every
> mdrun. What
> troubles me is the randomness with which -append
> fails/works.
> For eg, I have a simulation which
> runs from 3ns, 1ps in 1
> mdrun. Now oddly enough, the logfile starts from
> 1184ps(in
> the end, I do remember the one starting from 0
> but that
> was overwritten it seems) and the rest is
> appended uptil
> the 3000ps step. Why would append work from 1184ps to
> 3000ps but not for the previous ones?Could it have
> anything to do with the network/cluster? If that
> is the
> case is it safer to create a new file everytime
> and then
> concatenate them after say every 100ps?
> Pooja
> On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham
> <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>>
>
> wrote:
>
> On 30/01/2011 10:39 AM, Sai Pooja wrote:
>
> I would be happy to supply more
> information.. if
> someone could please look into this..
> otherwise I
> will have to switch to storing every file
> and then
> just concatenating them which seems like
> a rather
> roundabout way of doing it.
>
>
> As I suggested a few emails ago, are you sure
> that
> -cpi file exists? If your numerical suffixes are
> indexing restarts, then unless you've done
> some manual
> copying that you haven't told us about, it
> won't. Your
> filename scheme seems a bit contorted - like
> you're
> trying to do the work that GROMACS 4.5.x will
> just do
> for you if you let it.
>
> Otherwise, you'll have to do some detective
> work with
> gmxcheck on the -cpi to see what might be the
> issue.
>
> In your case, an initial
>
> mdrun -deffnm rex_3
>
> (perhaps save some copies while you're
> experimenting)
> and subsequently
>
> tpbconv -extend <blah> -f rex_3 -o rex_3
> mdrun -deffnm rex_3 -append
>
> will work and be much simpler than whatever
> you're
> trying to do with filenames :-)
>
> Mark
>
>
>
> On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja
> <saipooja at gmail.com
> <mailto:saipooja at gmail.com> <mailto:saipooja at gmail.com
> <mailto:saipooja at gmail.com>>> wrote:
>
> This is the command:
> nbs submit -command
>
> "(/usr/local/gromacs/4.5.1/bin/mdrun_mpi -s
> rex_3.tpr -e rex_3 -c after_rex_3
> -cpi restart3
> -cpo restart3 -ap
> pend -g rexlog3 -x rextraj3);" -nproc
> 1 -name
> "GENHAM-DIHEDRAL-3" -mail start end
> Pooja
>
> On Fri, Jan 28, 2011 at 4:20 PM, Mark
> Abraham
> <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>> wrote:
>
> On 29/01/2011 3:56 AM, Sai Pooja
> wrote:
>
> Hi,
> I am using tpbconv and mdrun
> to extend a
> simulation. I use it with the
> append
> option but the files still get
> overwritten or erased. Can
> someone help
> me in this regard?
> Pooja
> Commands (in python)
> cmd = '(%s/tpbconv -extend %f -s
> rex_%d.tpr -o rex_%d.tpr)'
> %(GROMPATH,dtstep,i,i)
> os.system(cmd)
> time.sleep(1)
> cmd = 'nbs submit
> -command "'
> cmd += '(%s/mdrun_mpi -noh
> -noversion -s rex_%d.tpr -e
> rex_%d -c
> after_rex_%d -cpi restart%d -cpo
> restart%d -append -g rexlog%d -x
> rextraj%d >/dev/null); '
> %(GROMPATH,i,i,i,i,i,i,i)
> cmd += '" '
> cmd += '-nproc 1 '
> cmd += '-name
> "GENHAM-DIHEDRAL-%d" '%(i)
> cmd += '-mail start end '
> cmd += '-elapsed_limit
> 16h >> rexid'
> os.system(cmd)
>
>
> More useful for diagnostic and
> record-preservation purposes is
> to construct
> the cmd string and print it to
> stdout (or
> something).
>
> At the moment it is far from
> clear that your
> -cpi file exists for the new run.
>
> Mark
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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