After running for 100 ps, I visualized the pullf_umbrella.xvg, in this plot I found the F value around 100 kJ/mol/ns. But force constant which I had set in md_US.mdp file was 4000 KJ/mol/ns. Does this difference show me that the US has not done properly?
;define = -DPOSRES integrator = md ; leap-frog integrator nsteps =100000 ; 1 * 100000 = 100 ps dt = 0.001 ; 1 fs nstcomm = 10 tinit = 0 ; Output control nstxout = 5000 ; save coordinates every 100 ps nstvout = 5000 ; save velocities every 100 ps nstenergy = 1000 ; save energies every 2 ps nstfout = 5000 nstxtcout = 5000 ; every 10 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-5 optimize_fft = yes ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = POPC pull_group1 = Ces_ion pull_init1 = 0.0 0.0 0.0 pull_rate1 = 0.0 0.0 0.00 pull_vec1 = 0 0 1 pull_k1 = 4000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution refcoord_scaling = com Would you please let me know your suggestions ? Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com> Cc: Sent: Wednesday, July 24, 2013 9:41 PM Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion On 7/24/13 11:53 AM, Shima Arasteh wrote: > Yes, Thanks. > > Would you give me a hint on this fact that how I would be sure that I am > running a correct US ? with proper settings? Either the restraint distance is maintained with acceptable sampling around that distance (given the force constant) or it's not. > To save time, I' d prefer to run the US.mdp just for one window. Do you agree > with me that if I run an incorrect US for any of the windows, I would get an > odd result for npt_US or md_US? > It should be pretty easy to see. -Justin > Many many thanks for your time and suggestions. > > > Sincerely, > Shima > > > ----- Original Message ----- > From: Justin Lemkul <jalem...@vt.edu> > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS > users <gmx-users@gromacs.org> > Cc: > Sent: Wednesday, July 24, 2013 8:05 PM > Subject: Re: [gmx-users] Umbrella Sampling _ pulled ion > > > > On 7/24/13 11:30 AM, Shima Arasteh wrote: >> Hi, >> >> I am trying to run US on a system composed of lipid bilayer/ ion/ water/ >> peptide. The peptide is inserted through the lipid bilayer and I' d like to >> study the ion conduction through the peptide across the membrane. >> >> In order to do so, I tried to set a specific ion ( Ces with the atom number >> 85563) as the pull_group1 in mdp file: >> pull_group1 = Ces_ion >> >> So I had to get a new group named Ces_ion contains of Ces 85563. Therefore >> made a new index file ( index_US.ndx). In this ndx file, there is an extra >> group in addition of existed groups as this( The last 2 lines in ndx file) : >> >> [ system] >> ... >> [protein] >> ... >> [protein-H] >> ... >> >> >> [ Ces_ion ] >> 85563 >> >> But after running the grompp, I get this fatal error: >> File input/output error: >> index_US.ndx >> >> >> Would you please let me know how I would be able to define a new group for a >> specific ion ? >> Did I make a mistake in defining a new group? > > What you did in terms of index group content is fine. The error message means > that the file called "index_US.ndx" is not present in the working directory, > or > it has the wrong permissions. > > -Justin > -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
