[gmx-users] mdrun error

Hector Mrz-Seara Monne hseara at netscape.net
Sat Oct 2 15:12:10 CEST 2004

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                =

>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:

; 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.         
>>    3.07715e+04    6.36605e+03    2.02562e+03    1.27192e+03   
>>     Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb
>>   -4.35088e+03   -4.18427e+04   -3.79469e+03   -2.96826e+02  
>>   Coulomb (LR)      Potential    Kinetic En.   Total Energy   
>>    3.08142e+02   -1.78960e+03    3.78781e+04    3.60885e+04   
>> 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 
>>gmx-users mailing list
>>gmx-users at gromacs.org
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