Then it looks there is bug ater define the constraints in itp file, bond distance changes.
On Wed, August 4, 2010 10:22 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Its oscillate between +/- 3-4 A. >> If I freeze the distance by using freeze groups and dim in mdp file. It >> works perfectly for NVT simulations. It oscillate for NPT simulation. > > I don't know if there have been any changes (I don't see anything in the > revision history), but as far as I know, freezing is incompatible with NPT > ensembles due to the inability to scale the frozen coordinates. > > -Justin > > >> Nilesh >> >> >> On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote: >> >> >>> Nilesh Dhumal wrote: >>> >>> >>>> constraints = all-bonds is working. I have solvent molecule for >>>> which I don't want constraints on them. I can't use constraints = >>>> all-bonds for simulation. >>> So you used g_dist to determine the distances with the setup shown >>> below, but did you correct for PBC effects? Is there a systematic >>> increase in the distance between the two particles, or does it >>> oscillate? >>> >>> -Justin >>> >>> >>> >>>> Nilesh >>>> >>>> >>>> >>>> On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote: >>>> >>>> >>>> >>>>> Nilesh Dhumal wrote: >>>>> >>>>> >>>>> >>>>>> Hello >>>>>> I am trying to constraints of a bond. I checked the distance >>>>>> using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone >>>>>> tell why it changes. Here I have pasted mdp file and itp file. >>>>>> >>>>> Maybe there's a bug in the interpretation of the constraints? >>>>> The >>>>> combination of "constraints = none" + [constraints] directive >>>>> should constrain the bond. Have you tried simply defining a >>>>> [bonds] >>>>> directive and using "constraints = all-bonds"? >>>>> >>>>> -Justin >>>>> >>>>> >>>>> >>>>> >>>>>> Nilesh >>>>>> Solvent.itp >>>>>> ; Derived from parsing of runfiles/alat.top.orig >>>>>> [ defaults ] >>>>>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >>>>>> ;1 3 yes 0.5 0.5 >>>>>> ; comb-rule 3 is square-root sigma, the OPLSAA version >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> [ atomtypes ] >>>>>> ; full atom descriptions are available in ffoplsaa.atp >>>>>> ; name bond_type mass charge ptype sigma >>>>>> epsilon opls_997 PA 0 100.0000 1.000 A >>>>>> 0.40000e-01 >>>>>> 0.82890e-01 >>>>>> opls_998 NE 0 100.0000 -1.000 A 0.40000e-01 >>>>>> 0.82890e-01 >>>>>> >>>>>> >>>>>> >>>>>> [ bondtypes ] >>>>>> ; i j func b0 kb >>>>>> PA NE 1 0.350000 000000 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> [ moleculetype ] >>>>>> ; name nrexcl >>>>>> ABC 3 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> [ atoms ] >>>>>> ; nr type resnr residu atom cgnr charge mass >>>>>> 1 opls_997 1 ABC PA 1 1.0000 >>>>>> 100.0000 >>>>>> 2 opls_998 1 ABC NE 1 -1.0000 >>>>>> 100.000 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> [ constraints ] >>>>>> 1 2 1 0.35000 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> pr.mdp title = cpeptid position restraining cpp >>>>>> = >>>>>> /usr/bin/cpp >>>>>> constraints = none integrator = md dt = >>>>>> 0.001 >>>>>> ; ps ! >>>>>> nsteps = 250000 ; total 1.0 ps. nstcomm = >>>>>> 1 >>>>>> nstxout = 10 nstvout = 1000 nstfout = >>>>>> 0 >>>>>> nstlog = 10 nstenergy = 10 nstlist = >>>>>> 10 >>>>>> ns_type = grid rlist = 1.0 >>>>>> coulombtype = PME >>>>>> vdwtype = cut-off rcoulomb = 1.0 rvdw = >>>>>> 1.4 >>>>>> fourierspacing = 0.12 fourier_nx = 0 >>>>>> fourier_ny = 0 >>>>>> fourier_nz = 0 pme_order = 4 ewald_rtol = >>>>>> 1e-5 >>>>>> optimize_fft = yes constraint-algorithm = SHAKE ; >>>>>> Berendsen >>>>>> temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 >>>>>> tc-grps =system ref_t = 400 ; Pressure coupling is not on >>>>>> Pcoupl = no >>>>>> pcoupltype = isotropic tau_p = 0.5 >>>>>> compressibility = 4.5e-5 ref_p = 1.0 ; Generate >>>>>> velocites is on at 300 K. gen_vel = yes gen_temp >>>>>> = 400.0 gen_seed = >>>>>> 173529 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> >>>>> >>>>> >>>>> Justin A. Lemkul >>>>> Ph.D. Candidate >>>>> ICTAS Doctoral Scholar >>>>> MILES-IGERT Trainee >>>>> 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 >>>>> 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-requ...@gromacs.org. >>>>> Can't >>>>> post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> 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 >>> 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-requ...@gromacs.org. Can't >>> post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >>> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 > 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-requ...@gromacs.org. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.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-requ...@gromacs.org. Can't post? 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