[gmx-users] mdrun seems stuck
nazoia at det.uminho.pt
Tue Jun 2 12:52:45 CEST 2009
Take a look to your .log file. Gromacs writes everything there.
On Tue, 2009-06-02 at 10:45 +0100, Stefano Meliga wrote:
> I'd like to run a position restrained MD of a protein in water with
> 3000 (protein) + 40000 (SOL) atoms.
> I preprocess the input with the command line:
> $grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro
> -p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr
> 4AKEprePRMD.mdp is:
> title = 4AKE_PRMD
> cpp = /usr/bin/cpp
> define = -DPOSRES
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 5000 ; total 10.0 ps.
> nstcomm = 1 ; [steps] frequency for center of mass
> motion removal
> nstxout = 100 ; [steps] frequency to write
> coordinates to output trajectory file
> nstvout = 100 ; [steps] frequency to write
> velocities to output trajectory
> nstfout = 0 ; [steps] frequency to write forces to
> output trajectory
> nstlog = 10 ; [steps] frequency to write energies
> to log file
> nstenergy = 10 ; [steps] frequency to write energies
> to energy file
> nstlist = 5 ; neighbour searching
> ns_type = grid
> rlist = 1.0
> coulombtype = EWALD
> rcoulomb = 1.0
> vdwtype = Cut-off
> rvdw = 1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = berendsen
> tau_t = 0.1 0.1
> tc-grps = Protein Non-Protein
> ref_t = 300 300
> ; Energy monitoring
> energygrps = Protein SOL
> ; Pressure coupling is on
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5 ; [1/bar] compressibility of water
> ref_p = 1.0 ; [bar] reference pressure for coupling
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
> Then I run the PR MD:
> $grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e
> 4AKE_PRMD.edr -g 4AKE_PRMD.log -v
> These lines appear on the terminal:
> starting mdrun 'Protein in water'
> 5000 steps, 10.0 ps.
> ...but from this point on nothing more is displayed. I see neither
> steps nor time left.
> Are the parameter in the mdp file defining a too expensive simulation?
> I've tryied removing pressure and temperature coupling but the problem remains.
> How can I solve this issue?
> -DPOSRES refers to posre.itp, I guess. posre.itp was created from the
> original pdb before the energy minimization. Should I run pdb2gmx once
> again after the EM to create a new posre.itp?
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Nuno Gonçalo Azoia Lopes
Finishing Research Laboratory
Textile Engineering Department
Universidade do Minho
Campus de Azurém
Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293
Mobile: +351 965 382 487
E-mail: nazoia at det.uminho.pt
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