hello Here they are the command line and mdp file. I use Gromacs 4.5.3. This is a test case only and the protein is 1UBQ. Grompp wills top for about 10 minutes then go through.
***********output of grompp***************** Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6# Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Coupling 1 copies of molecule type 'Protein' Setting gen_seed to 8552 Velocities were taken from a Maxwell distribution at 300 K ******************************** Command line and mdp file: ****************************** grompp -f pr1.mdp -c after_em.gro -t em.trr -p topol.top -o pr1 ****************************** define = -DPOSRES ; position restrain the protein ; Run parameters integrator = sd ; leap-frog integrator nsteps = 5000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 5000 ; save velocities every 100ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = hbonds ; H bonds constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 10 ; 20 fs rlist = 0.8 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.8 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ;free energy stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 sc_alpha =0.5 sc-power =1.0 sc-sigma = 0.3 couple-moltype = Protein couple-lambda0 = vdw-q couple-lambda1 = none ******************************* thanks. dawei On Mon, Feb 7, 2011 at 1:05 PM, TJ Mustard <musta...@onid.orst.edu> wrote: > Dawei, > > > > I have no problems with proteins in the thousands of atoms. Can you post > your command line and mdp files? > > > > Thank you, > > TJ Mustard > > On February 7, 2011 at 9:31 AM Da-Wei Li <lida...@gmail.com> wrote: > > Well. It actually isn't dead but becomes very slow for large proteins. > dawei > > On Mon, Feb 7, 2011 at 11:44 AM, Da-Wei Li <lida...@gmail.com> wrote: > > hi, > I did more test and found that it depended on size of the protein. Grompp > will die when number of atoms of the protein is larger than about 200. Is it > possible the source code limit the size of the protein that can be > decoupled? > thanks. > dawei > > > On Mon, Feb 7, 2011 at 10:34 AM, Da-Wei Li <lida...@gmail.com> wrote: > > Dear users > I tried free energy calculation but grompp couldn't go through. It stops > after > ******************* > Generated 2278 of the 2278 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 2278 of the 2278 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein' > turning H bonds into constraints... > Excluding 2 bonded neighbours molecule type 'SOL' > turning H bonds into constraints... > Excluding 1 bonded neighbours molecule type 'CL' > turning H bonds into constraints... > Coupling 1 copies of molecule type 'Protein' > ******************* > The CPU usage is 100%. > I just add following into the mdp file: > *************** > free_energy = yes > init_lambda = 0.0 > delta_lambda = 0 > sc_alpha =0.5 > sc-power =1.0 > sc-sigma = 0.3 > couple-moltype = Protein > couple-lambda0 = vdw-q > couple-lambda1 = none > *************** > Does anyone have some idea about this problem? thanks. > Another question is whether I can switch off "two molecules" (such as > protein+ligand) in free energy calculation? I searched this list and got > that 4.0.7 did support this. how about 4.5.4? > dawei > > > > > TJ Mustard > Email: musta...@onid.orst.edu > > -- > 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 >
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