[gmx-users] mdrun seems stuck

[Stefano Meliga]

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.

Stefano

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:
>   
>> 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
>>