[gmx-users] mdrun error

[David]

> > 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.
> 
First off, please turn off the weird fonts in your mail...

In the improper definition below there are too many force constants,
i.e. the thirs and sixth number (m) should go. Further the force
constant is ten times higher than usual which means vibrations will be
sqrt(10) times faster, which again means you will have to reduce the
timestep. Reducing the force constant by a factor of ten will be fine
too. 
> .....
>  [ 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
>   
> 
> 
> ______________________________________________________________________
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++