[gmx-users] mdrun error

Sat Oct 2 20:11:45 CEST 2004

spoel at xray.bmc.uu.se wrote:

>On Sat, 2004-10-02 at 16:48, Hector Mrz-Seara Monne wrote:
>  
>
>>>>    
>>>>        
>>>>
>>>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.
>>    
>>
>
>Try equilibrating at lower temperature and/or with a shorter time step.
>In particular since you describe this resonance thing. Could it be that
>your force constants are too high? You should have roughly 20 time steps
>in a complete period of the fastest motion.
>
>
>  
>
Thanks in advance for all your help, it's been quite useful for me in 
order to increase my knowledge on this suite.
I've been thinking in the last suggestion and I'm not sure about the 
meaning. As I understand if I use high constants
for defining my proper dihedrals I have to reduce my time steep that 
actually is quite small 1fs only or work at lower temperature.
Here the *.itp file of the monomer contain this lines that I have 
specifically modify to have a planarity system.

.....
 [ dihedrals ]
 ;ai  aj  ak  al  fu    c0    c1 m  c0   c1 m
  9    12  10   8    2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBA  CAD  
CAE  CAU
  14  15  13  11   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBB  NAV  
CAF  CAG
  17  16  20  18   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBC  NAW  
CAH  CAI
  22  23  21  19   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBD  OAY  
CAJ  CAK
  27  26  29  28   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAZ  CAT  
OAX  OAC
  17  18  19  22   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBC  CAI  
CAK  CBD
  18  19  22  21   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAI  CAK  
CBD  CAJ
  19  22  21  20   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAK  CBD  
CAJ  CAH
  22  21  20  17   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBD  CAJ  
CAH  CBC
  21  20  17  18   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAJ  CAH  
CBC  CAI
  20  17  18  19   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAH  CBC  
CAI  CAK
   9   10  11  14   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBA  CAE  
CAG  CBB
  10  11  14  13   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAE  CAG  
CBB  CAF
  11  14  13  12   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAG  CBB  
CAF  CAD
  14  13  12   9    2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBB  CAF  
CAD  CBA
  14  15  17  16   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CBB  NAV  
CBC  NAW
  13  12   9   10   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAF  CAD  
CBA  CAE
  12   9  10   11   2   0.0 1673.6 0   0.0 1673.6 0 ; IDI   CAD  CBA  
CAE  CAG
   4    3    2    1    1   0.0       5.9 3   0.0       5.9 3 ; DI    
CAN  CAM  CAL  CAA
.....
  11  14  15  16   1 180.0   53.5 2 180.0   33.5 2 ; DI    CAG  CBB  
NAV  NAW *
  15  16  17  20   1 180.0   53.5 2 180.0   33.5 2 ; DI    NAV  NAW  
CBC  CAH *
.....
  25  26  27  29   1     0.0     0.4 6     0.0     0.4 6 ; DI    CAR  
CAT  CAZ  OAX
  26  27  29  30   1 180.0   16.7 2 180.0   16.7 2 ; DI    CAT  CAZ  
OAX  HE2  *

Do you know if your advise works equally for both proper and improper 
dihedrals?  If not can you tell me the diference?
I think for your coment that the dihedral with the asterisk that are the 
problematic? witch time step will you use, or do you know any
way to avoid the restriction that my system contain?

Thank you very much for taking your time to answer me, David. If you 
think you need any other information or that is not clear what
 I'm asking for just tell me and I can send you any indormation or foles 
that you thing could be usefull to solve my actual problems

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20041002/0654b5f1/attachment.html>