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. 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 > > > -- 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
