Exactly so. But in the ffbonded.itp file there are two columns, equilibrium bond length and Kb . So evenif I give zero then it won't affect the bond . Thanks a lot for the reply, it's working fine now . On Mon, Jul 23, 2012 at 6:02 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/23/12 8:31 AM, tarak karmakar wrote: >> >> 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 ??? >> > > Constraints make bonds rigid. The force constant is irrelevant. > > -Justin > > >> 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 >> >> >> >> > > -- > ======================================== > > 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