[gmx-users] dihedral parameters in oplsaa
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 27 12:23:35 CEST 2008
friendli wrote:
> No. there is no warning in grompp.
>
then finally, are these parameters specified as zero in the
ffoplsaabon.itp file?
In that case it is probably correct.
> thanks
>
>
>
> Message: 2
> Date: Tue, 27 May 2008 11:17:21 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] dihedral parameters in oplsaa
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <483BD1A1.2090305 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> friendli wrote:
>
>> > Thanks David and Mark for the advice. But I think I did not state it
>> > very clearly.
>> > > It is not 9 sets of dihedrals which share the same parameters are
>> found > in the output by gmxdump. But 9 of the 15 dihedrals exist in
>> this > molecule are listed. They are under Ryckaert-Bell. As for the
>> function > types, there are only two.
>> > > I pastes the relevant part this time. The missing parameter
>> dihedrals > are labeled with ; **.
>>
>
> Then most likely they have parameters that are zero. Do you get grompp
> warnings about this?
>
>
>> > > from .top file,
>> > [ dihedrals ]
>> > ; ai aj ak al funct c0 c1
>> > c2 c3 c4 c5
>> > 2 1 5 6 3
>> > 2 1 5 7 3
>> > 2 1 5 8 3
>> > 3 1 5 6 3
>> > 3 1 5 7 3
>> > 3 1 5 8 3
>> > 4 1 5 6 3
>> > 4 1 5 7 3
>> > 4 1 5 8 3
>> > 1 5 8 9 3 ; **
>> > 1 5 8 10 3 ; **
>> > 6 5 8 9 3 ; **
>> > 6 5 8 10 3 ; **
>> > 7 5 8 9 3 ; **
>> > 7 5 8 10 3 ; **
>> > ___________________________________________
>> > from gmxdump,
>> > Ryckaert-Bell.:
>> > nr: 45
>> > multinr[division over processors]: 45
>> > iatoms:
>> > 0 type=47 (RBDIHS) 1 0 4 5
>> > 1 type=47 (RBDIHS) 1 0 4 6
>> > 2 type=48 (RBDIHS) 1 0 4 7
>> > 3 type=47 (RBDIHS) 2 0 4 5
>> > 4 type=47 (RBDIHS) 2 0 4 6
>> > 5 type=48 (RBDIHS) 2 0 4 7
>> > 6 type=47 (RBDIHS) 3 0 4 5
>> > 7 type=47 (RBDIHS) 3 0 4 6
>> > 8 type=48 (RBDIHS) 3 0 4 7
>> > _____________________________________________
>> > for identify the atom numbers,
>> > [ atoms ]
>> > ; nr type resnr residue atom cgnr charge mass
>> > typeB chargeB massB
>> > 1 opls_287 1 GLY N 1 -0.3 14.0067
>> ; > qtot -0.3
>> > 2 opls_290 1 GLY H1 1 0.33 1.008
>> ; > qtot 0.03
>> > 3 opls_290 1 GLY H2 1 0.33 1.008
>> ; > qtot 0.36
>> > 4 opls_290 1 GLY H3 1 0.33 1.008
>> ; > qtot 0.69
>> > 5 opls_298 1 GLY CA 1 0.09 12.011
>> ; > qtot 0.78
>> > 6 opls_140 1 GLY HA1 1 0.06 1.008
>> ; > qtot 0.84
>> > 7 opls_140 1 GLY HA2 1 0.06 1.008
>> ; > qtot 0.9
>> > 8 opls_271 1 GLY C 2 0.7 12.011
>> ; > qtot 1.6
>> > 9 opls_272 1 GLY O1 2 -0.8 15.9994
>> ; > qtot 0.8
>> > 10 opls_272 1 GLY O2 2 -0.8 15.9994
>> ; > qtot 0
>> > > > regards
>> > > LQ
>>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
More information about the gromacs.org_gmx-users
mailing list