[gmx-users] mdrun seems stuck

[Nuno Azoia]

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:
> Hello,
> 
> 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?
> 
> Thanks,
> 
> Stefano
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 
Nuno Gonçalo Azoia Lopes
 
Finishing Research Laboratory
Textile Engineering Department
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal
 
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