[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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