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. 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 > > > -- 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
