Thanks for the reply. But then what should I give as Kb [ bond stretching constant ] in the ffbonded.itp file ? should I give 00.000 there or something else ???
On Mon, Jul 23, 2012 at 4:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/23/12 2:39 AM, tarak karmakar wrote: >> >> Dear All, >> >> >> In my simulation I want to fix the S=O bond length of SO2, but the >> angle has to be kept flexible. So I search for the distance restraints >> in gromacs mailing list and >> accordingly I have incorporated the distant_restraints block in the >> topology file. After a short equilibration, when I am seeing the movie >> of the trajectory, the bond length is changing. So what is the right >> way to keep the distance fixed and the angle flexible ? > > > Use constraints for the bonds, not distance restraints. > > -Justin > > >> Part of the topology file is as follows >> >> >> ; Include forcefield parameters >> #include "./amber94ff/forcefield.itp" >> >> [ moleculetype ] >> ; Name nrexcl >> Other_chain_A 3 >> >> [ atoms ] >> ; nr type resnr residue atom cgnr charge mass >> typeB chargeB massB >> ; residue 502 SR rtp CR q 0.0 >> 1 S 502 SR S 1 0.6512 32.07 ; >> qtot 0.6512 >> 2 O 502 SR O1 2 -0.3256 16 ; >> qtot 0.3256 >> 3 O 502 SR O2 3 -0.3256 16 ; >> qtot 0 >> >> [ bonds ] >> ; ai aj funct c0 c1 c2 c3 >> 1 2 1 >> 1 3 1 >> >> [ distance_restraints ] >> ; ai aj type index type' low up1 up2 fac >> 1 2 1 0 1 1.149 1.490 1.490 1.0 >> 1 3 1 0 1 1.149 1.490 1.490 1.0 >> >> [ angles ] >> ; ai aj ak funct c0 c1 c2 >> c3 >> 2 1 3 1 >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Include water topology >> #include "./amber94.ff/spc.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include topology for ions >> #include "./amber94.ff/ions.itp" >> >> [ system ] >> ; Name >> Protein in water >> >> [ molecules ] >> ; Compound #mols >> Other_chain_A 1 >> SOL 622 >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
