[gmx-users] mdrun seems stuck
smeliga at gmail.com
Tue Jun 2 12:13:41 CEST 2009
The simulation seems just very slow.
step 0 has appeared on the screen after several minutes and in the log
file there's only step zero as well.
Nuno Azoia ha scritto:
> Take a look to your .log file. Gromacs writes everything there.
> Nuno Azoia
> 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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