Thank you for your suggestions, Berk, > Are you sure your initial distance is -3.5 along (0,0,-1), > this means the distance is actually +3.5 in z.
I am sure that. I want to set a molecule +3.5 in z from center of the bilayer. > Another issue could be that 3.5 is more than half the box size. > I think we should add a check for too long distances, > so users get a clear error message and they do not need to contact > the mailing list. > > Berk My box size is approximately 8.0 nm. So, +3.5 is not more than half of the box in my case. And also, when I tried +2.1 nm (just above lipid head groups), the same errors and warnings were observed. Is there other possible problems? Hideya >> Date: Wed, 9 Sep 2009 13:18:04 -0400 >> From: [email protected] >> To: [email protected] >> Subject: [gmx-users] Errors in constraint pulling >> >> Dear GROMACS users, >> >> I am trying to calculate the potential of mean force (PMF) of a >> molecule (A) across phospholipid bilayer (LIP) using constraint >> method. >> I am using GROMACS ver 4.0.4. >> RUN parameters are as follows >> >> ------------------------------------------------------------------------------- >> integrator = md >> tinit = 0 >> dt = 0.002 ;[ps] >> nstlist = 10 ;[step] >> ns_type = grid >> rlist = 1.0 >> pbc = xyz >> >> coulombtype = pme >> rcoulomb = 1.0 ;[nm] >> epsilon-r = 1 ;(1) >> vdw-type = switch >> rvdw-switch = 0.9 ;[nm] >> rvdw = 1.0 ;[nm] >> DispCorr = EnerPres >> >> fourierspacing = 0.12 ;[nm] (0.12) >> fourier_nx = 0 ;(0) >> fourier_ny = 0 ;(0) >> fourier_nz = 0 ;(0) >> pme_order = 4 ;(4) >> ewald_rtol = 1e-05 ;(1e-5) >> epsilon_surface = 0 ;(0) >> optimize_fft = no >> >> tcoupl = berendsen >> tc_grps = LIP SOL A >> tau_t = 0.1 0.1 0.1 ;[ps] >> ref_t = 300 300 300 ;[K] >> Pcoupl = berendsen >> Pcoupltype = semiisotropic ;useful for membrane >> tau_p = 1.0 1.0 ;[ps] >> compressibility = 4.5e-05 4.5e-05 ;[bar^-1] >> ref_p = 1.0 1.0 ;[bar] >> >> gen_vel = no ;yes or no >> gen_temp = 300 ;[K] >> gen_seed = 113 ;(173529) >> >> constraints = all-bonds ;all-bonds/none >> constraint-algorithm = LINCS >> unconstrained-start = no >> lincs-order = 4 ;(4) >> lincs-warnangle = 30 ;(30) >> >> ; COM PULLING >> pull = constraint >> pull_geometry = direction >> pull_dim = N N Y >> pullstart = no >> pull_nstxout = 10 >> pull_nstfout = 10 >> pull_ngroups = 1 >> pull_group0 = LIP >> pull_group1 = A >> pull_vec1 = 0.0 0.0 -1.0 >> pull_init1 = -3.50 >> pull_rate1 = 0 >> pull_k1 = 500 >> >> ------------------------------------------------------------------------------- >> When I simulated under above parameters, following warnings and errors >> were generated. >> >> -Warning: pressure scaling more than 1% >> -LINCS warning: >> >> These errors were always generated when a molecule (pull_gropu1) was >> existing in water phase. >> After simulation, serious disruption of a molecule (pull_gropu1) was >> observed. >> >> However, when a molecule (pull_gropu1) was existing inside lipid >> membrane, no error was observed and calculation was successfully >> conducted in constrained simulation. >> >> I have done long time (5 nsec) simulations before constrained >> simulation using umbrella method, thus I believe the initial condition >> is fully equilibrated. >> >> Could some one please give me an advice to calculate PMF? >> >> Sincerely >> >> >> ___________________________________________________________________ >> Hideya Nakamura, Ph.D. >> >> Post Doctoral Associate >> University of Florida, Particle Engineering Research Center (PERC) >> mail to: [email protected] >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > ________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
