[gmx-users] mdrun error
Hector Mrz-Seara Monne
hseara at netscape.net
Sat Oct 2 16:48:30 CEST 2004
spoel at xray.bmc.uu.se wrote:
>On Sat, 2004-10-02 at 15:12, Hector Mrz-Seara Monne wrote:
>
>
>>spoel at xray.bmc.uu.se wrote:
>>
>>
>>>On Sat, 2004-10-02 at 13:39, Hector Mrz-Seara Monne wrote:
>>>
>>>
>>>
>>>>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:
>>>>
>>>>
>>>>
>>>>
>>>Have you stopped the center of mass motion? Sometimes it ahs to be done
>>>per group (e.g. monolayer and water).
>>>
>>>
>>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 =
>>
>>
>
>OK that looks fine. Have you verified (md.log file) that these settings
>have been incorporated in the tpr file?
>
It seems that every thing is ok
>
>Have you tried visualising the trajectory?
>
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.
>
>Do you have periodic boundary conditions? Otherwise you might want to
>set comm-mode = angular
>
>
I use periodic boundary conditions
>
>
>>
>>
>>
>>>Also your temperature is 450 K. Do you have T coupling turned on?
>>>
>>>
>>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
>>
>>
>>>
>>>
>>>
>>>> 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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>>>>
>>>>
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