On 4/28/2011 5:47 PM, Anna Marabotti wrote:
Dear Justin,
thank you for your precious help. Yes, the problem is what you say and what
I was suspecting too (but I was not sure, that's why I was searching for a
confirmation of my suspects from more expert people). The problem however is
present in the NVT->NPT junction. My .mdp settings were
NVT:
tinit = 0
init_step = 0
nsteps = 10000
dt = 0.002
NPT
tinit = 0
init_step = 20000 (instead of 10000)
nsteps = 50000
dt = 0.002
That's why I had a last NPT step of 70000 instead of 60000, and that's why I
set init_step = 70000 in the production MD.
What you are saying also explains the anomalous behaviour of the xvg file
created from the .edr file, in which only few points were saved, therefore
the graphs created with xmgrace contain only 7 values (at 140, 200, 300 400,
5140, 10140, 15140 ps).
I always set nstep identical to the last step of the previous equilibration
MD because I understood that it was necessary to do it to obtain an exact
continuation, there is no other special reason.
The label on the step number has nothing to do with the physics.
Instructions for restarts preserving simulation ensembles are on the
website. IIRC init_step refers to the label given to the step whose time
is tinit (see manual 7.3.3), and haphazardly changing only one of them
might lead to such problems.
Since you are saying that
this is no (longer?) necessary (I'm currently using Gromacs 4.0.7 on this
machine), I'm very happy to set always nsteps = 0, to avoid future mistakes.
Do that.
In the meantime, what I have to do? I had a look at the .xtc files with
gmxcheck and apparently all is fine, with no error messages, also the
trajectory seems to be coherent with my expectations. I run g_rms and
g_gyrate and the behaviour of the systems appears "normal" (apart from the
fact that the system is not stabilized yet, so I have to continue the
trajectory). I can provide you (offlist) the .xvg graphs, if you want.
Based on these data, what do you suggest to do? Do you think that the
simulation could be considered formally correct (i.e. this is only a problem
of erroneous writing of .edr file) or do I have to repeat
(AAAAAARRRRRRGGGGHHHHH) the whole simulation? I saw in the manual that the
option -rerun of mdrun command allows to recalculate forces and energies
from a trajectory file, do you think that I can use it to obtain a new .edr
file?
If it's just a problem of labelling the frames, then trjcat and eneconv
have -settime to deal with these kinds of scenarios.
Mark
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