[gmx-users] Continuation 1) after crash and 2) in general

[Marc Baaden]

Hi,

in a recent message spoel at xray.bmc.uu.se said:
>> Kill the simulation and restart it from where the error in the xtc
>> started (tpbconv -s topol -f traj -o cont -time 10000000) Fill in the
>> right number for the time there. 

I tried the tbpconv on a crash that happened recently. My only concern
is, does it properly take into account shuffling ? Eg if the initial
simulation was shuffled, will the continuation run be shuffled in the
same way ?

And a more general question: if I want to split my simulation of let's
say 5 ns into chunks of 1 ns, what do I need in order to obtain the
same thing as in one long simulation, eg no "discontinuities" at the
simulation ends (1 ns intervals).

I mean, is it sufficient to write out coords+velocities at the end ?
(Because due to the integration algorithm they should be t/2 shifted
during a run, but what happens when you write them out ?)

Is there a kind of model "restart-mdp" file ?

And is it always necessary to build a complete topology when you
restart ? With eg AMBER you can use the same topology and just indicate
the new coords/vels to start from and which time it is.

Thanks in advance,

  Marc Baaden

-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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