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. 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 -- 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
