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<a class="moz-txt-link-abbreviated" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> wrote:<br>
<blockquote type="cite" cite="mid1096724155.8598.21.camel@h32n2fls34o1123.telia.com">
<pre wrap="">On Sat, 2004-10-02 at 15:12, Hector Mrz-Seara Monne wrote:
</pre>
<blockquote type="cite">
<pre wrap=""><a class="moz-txt-link-abbreviated" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Sat, 2004-10-02 at 13:39, Hector Mrz-Seara Monne wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello All,
Maybe the question that follow has been posted before but I wasn't
able to find it, then if anyone knows where just told me. My problem
is that my monolayer system is working well, but after a 1.7 ns of
dynamics with a step 1fs I get the following error:
</pre>
</blockquote>
<pre wrap="">Have you stopped the center of mass motion? Sometimes it ahs to be done
per group (e.g. monolayer and water).
</pre>
</blockquote>
<pre wrap="">This simulation was made in vacuum. Only de monomer here is the *.top
file:
#include "ffgmx.itp"
#include "azo_neutral.itp"
[ system ]
Neutral monomer Azobenzenos
[ molecules ]
DRG 225
And the part corresponding to the removal of the translation of CM in
the dyn.mdp is the following:
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
</pre>
</blockquote>
<pre wrap=""><!---->
OK that looks fine. Have you verified (md.log file) that these settings
have been incorporated in the tpr file?</pre>
</blockquote>
It seems that every thing is ok<br>
<blockquote type="cite" cite="mid1096724155.8598.21.camel@h32n2fls34o1123.telia.com">
<pre wrap="">
Have you tried visualising the trajectory?</pre>
</blockquote>
Every thing seems normal if you make a overall view. But after checking one
by one all the monomers one of them seem to kill itself.The main part of
the sistem is very rigid with many impropials defined along it, benzene-N=N-benzene
( it must be all in a plane). I notice when I was trying to parametrice the
molecule that if I try to keep it complete plane whit impropial then the
structure crash in a dyanmic, It seems like the molecule enter in a kind
of resonance effect that finish with unnatural bond legth and angles and
the crashing of the system. I pass through this problem changing some impropials
for propials with a loose in the planarity. It seems that this fenomenom
is crashing my system again. Have you any suggestion? Thank you.<br>
<br>
<blockquote type="cite" cite="mid1096724155.8598.21.camel@h32n2fls34o1123.telia.com">
<pre wrap="">
Do you have periodic boundary conditions? Otherwise you might want to
set comm-mode = angular
</pre>
</blockquote>
I use periodic boundary conditions<br>
<br>
<blockquote type="cite" cite="mid1096724155.8598.21.camel@h32n2fls34o1123.telia.com">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">Also your temperature is 450 K. Do you have T coupling turned on?
</pre>
</blockquote>
<pre wrap="">I think that something is not working well since in the bath is set to
300 K, in fact I have not notice that before posting my report, as
follow in the dyn.mdp:
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = no
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Random seed for Andersen thermostat
andersen_seed = 815131
Have you any sugestion? Thank you David
</pre>
<blockquote type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap=""> Step Time Lambda
1731000 1731.00012 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih.
LJ-14
3.07715e+04 6.36605e+03 2.02562e+03 1.27192e+03
2.39194e+04
Coulomb-14 LJ (SR) LJ (LR) Disper. corr. Coulomb
(SR)
-4.35088e+03 -4.18427e+04 -3.79469e+03 -2.96826e+02
-1.61672e+04
Coulomb (LR) Potential Kinetic En. Total Energy
Temperature
3.08142e+02 -1.78960e+03 3.78781e+04 3.60885e+04
4.50009e+02
Pressure (bar)
-4.24753e+02
Large VCM(group rest): 0.00172, -0.00977, -0.00129,
ekin-cm: 4.46633e+00
Large VCM(group rest): 0.00213, -0.00449, 0.00016,
ekin-cm: 1.10213e+00
Large VCM(group rest): 0.00437, -0.00540, -0.00333,
ekin-cm: 2.64588e+00
There were 90 inconsistent shifts. Check your topology
Large VCM(group rest): 0.00420, -0.00470, -0.00106,
ekin-cm: 1.82364e+00
There is anyone that with that information have any idea of what is
going on. I'm sorry but I can't understand this message. Check what of
the topology file. My topology file was made by PRODRG and extended by
me manually, The system are 255 monomers of
8C's-benzene-N=N-benzene-O-3C's-COOH monom in vacum. If you need
anything else just tell me.
Thanks in advance.
Hector Martínez-Seara Monné
Universidad Barcelona
Dpt. Química-Física
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