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@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@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-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
