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David van der Spoel wrote:
<blockquote
cite="midPine.LNX.4.44.0502092145530.32158-100000@rembrandt.bmc.uu.se"
type="cite">
<pre wrap="">On Wed, 9 Feb 2005, Attilio wrote:
</pre>
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<pre wrap="">I'm doing NPT md on my system, a small drug non covalently linked to
DNA, and I already performed 8.5 ns simulation.
At this point I get this message
</pre>
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</blockquote>
<blockquote
cite="midPine.LNX.4.44.0502092145530.32158-100000@rembrandt.bmc.uu.se"
type="cite">
<pre wrap="">the problem is that you have selected anisotropic pressure scaling. You'll
probably have to de redo the simulation with isotropic scaling. Do also
consider to use PME with a cut-off of 0.9 nm, and 0.9/1.4 for the
vanderwaals. It will be roughly equally fast and more accurate.
</pre>
</blockquote>
I cheched my input file, and this is the section corresponding to the P
coupling<br>
<br>
I; P COUPLING<br>
;<br>
pcoupl = Parrinello-Rahman<br>
compressibility = 4.5e-5<br>
tau_p = 1.0<br>
ref_p = 1.0<br>
pcoupltype = isotropic<br>
;<br>
<br>
I'm also using PME, with 1,2 cutoff.<br>
I was thinking to increase the frequency of removal for the
rototranslation of the center of mass of the system, or maybe I have to
change some parameter for the lincs algotrithm (that I applied only to
h-bonds)?<br>
Thanks<br>
Attilio<br>
<blockquote
cite="midPine.LNX.4.44.0502092145530.32158-100000@rembrandt.bmc.uu.se"
type="cite">
<pre wrap=""></pre>
<blockquote type="cite">
<pre wrap="">"Inertia tensor (3x3):
Inertia tensor[ 0]={ 4.61676e+03, 1.35627e+03, -2.24899e+03}
Inertia tensor[ 1]={ 1.35627e+03, 8.25089e+03, -3.82382e+02}
Inertia tensor[ 2]={-2.24899e+03, -3.82382e+02, 1.18415e+04}
t = 8898.120 ps: Water molecule starting at atom 11315 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Step 5932081, time 8898.12 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.000000 (between atoms 1 and 2) rms nan
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
t = 8898.121 ps: Water molecule starting at atom 11993 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Step 5932082, time 8898.12 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.000000 (between atoms 1 and 2) rms nan
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
t = 8898.123 ps: Water molecule starting at atom 11993 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
....
.....
....
t = 8898.141 ps: Water molecule starting at atom 11993 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
Grid: -2147483648 x -2147483648 x -2147483648 cells
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]"
I checked the simulation, and I see that the box, originally cubic,
transform to a rectangular box, so the minimum distance
between the images decrease abruptly from 35 to 15 angtroms, and the DNA
strands separate (it's beatiful to see,
not to report to your boss...).
I'm using a time step of 1.5 ps, and a cutoff of 12 angstrom for both
electrostatic and van der waals.
How may I go on without break my system?
Thanks in advance,
Attilio
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</pre>
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