[gmx-users] prodrg

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 4 11:28:57 CEST 2004


On Mon, 2004-10-04 at 08:13, Hector Mrz-Seara Monne wrote:
> Thank you David for your help, I'm quite new in gromacs and many things 
> still lack on
> my knowledge. Well I'm trying to reduce all the constants forces in the 
> *.itp file of my monomer.
> By the way, the only constants that worry you where those of the 
> improper dihedral or also of the proper once
> with the asterisk. And why PRODRG  duplicate the colums of definitions
> 
> (c0    c1 m)  (c0   c1 m)
> 
> , this is normal(this confuses me since the beginning)?
This has to do with free energy calculations where you go from one
definition to another. Does prodrg produce the m for impropers as well?

> 
> Thanks.
> 
> I've been looking for the configuration of my fonts and everything seems 
> to be allright. I'm using the netscape mail. I don't know
> what is hapenning but I'll try to fix this problem in the near future
> 
> spoel at xray.bmc.uu.se wrote:
> 
> >>>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
> >>  
> >>
> >>
> >>______________________________________________________________________
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> >>    
> >>
-- 
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
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