Hi all,
and thanks Mark, Chris and Xavier for your comments.
I finally managed to run the REMD simulation but i can not restart the
simulation or continue the simulation after it finished.
I tried with a test system and run two replicas for just 20 ps. After it
finished correctly i extended the time in each .tpr file
and tried to continue the REMD simulation using the checkpoint files but i
always get the same error message
Multi-checking simulation part ... OK
Multi-checking simulation part ... OK
Reading file test0.tpr, VERSION 4.5.5 (single precision)
Reading file test1.tpr, VERSION 4.5.5 (single precision)
Multi-checking simulation part ... Multi-checking simulation part ...
Multi-checking simulation part ... Multi-checking simulation part ...
Multi-checking simulation part ... Multi-checking simulation part ... ERROR:
0031-250 task 6: Segmentation fault
ERROR: 0031-250 task 7: Segmentation fault
ERROR: 0031-250 task 2: Segmentation fault
ERROR: 0031-250 task 1: Segmentation fault
ERROR: 0031-250 task 5: Segmentation fault
ERROR: 0031-250 task 3: Segmentation fault
ERROR: 0031-250 task 0: Terminated
ERROR: 0031-250 task 4: Terminated
I used Gromacs 4.5.5 and the following commands:
to start the REMD simulation:
mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500
to extend the time of the simulation in the .tpr files:
tpbconv_d -s test_#.tpr -extend 20 -o test_#.tpr
to continue the REMD simualtion:
mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500
Do i need to use any specific option to be able to continue the REMD simulation?
Thanks in advanced
Kenny
Virtual sites also have a hidden benefit - not only can you take a longer
time step, but the width of the distribution of PE is relatively wider, so
you can have higher exchange probability for the same temperatures.
Mark
On Tue, Nov 20, 2012 at 12:34 AM, Christopher Neale<
[email protected]> wrote:
> Xavier is right, except that you can also reduce the size of your system.
> You can take larger steps in temperature
> if you have fewer atoms. If you are using a cubic system, you can move to
> a rhombic dodecahedron.
> Even constraining all bonds will help a bit here (vs. harmonic bonds).
> There are lots of papers on this topic.
>
> To see why you don't get any exchanges, construct histograms of your
> potential energies and you will see
> that they don't overlap. Also, it is inefficient to take evenly spaced
> temperatures. This is not your major problem,
> but read a bit on exponentially spaced temperatures for REMD.
>
> Chris.
>
> -- original message --
>
> Well either you use more replicas or you reduce the temperature
> range ...
> There is no way around!
>
> On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote:
>
> > Dear All,
> >
> > i am trying to performed REMD simulations using Gromacs.
> > My question is concerning the temperature distribution and the
> > number of replica.
> > I need to run 24 replicas of my system with a temperature range of
> > 290-400 K. How can I select the temperatures values for each replica?
> > I tried the serverhttp://folding.bmc.uu.se/remd/index.php but for
> > my system it gives 50 replicas. If i try to take 24 evenly spaced
> > values from the obtained list of temperature then
> > the replicas do not exchange at all.
> > I am using Gromacs 4.5.5 and my system has 6862 water molecules and
> > 535 atoms for the solute.
> >
> > Thanks in advanced
> > Kenny
> >
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Kenny Bravo Rodriguez
Max-Planck-Institut für Kohlenforschung
Kaiser-Wilhelm-Platz 1
D-45470 Mülheim an der Ruhr
Germany
Phone: +49 (0)208 306 2160
Email:[email protected]
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