run an EM with flexible water. I often find that this is the only way
to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or
different depending on your water model I think) should be enough.
Chris.
Hi Chris and Justin,
On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
chris.neale at utoronto.ca wrote:
You'll need to provide a much better report than this if you want
to receive any useful help.
Copy and paste the exact commands of what you did
Copy and paste the exact log file and error messages
The command I had used (for both 4.0.7 and 4.5.4) are:
pdb2gmx -f 1EXR.pdb -o 1EXR.gro -water spc -ignh -p 1EXR.top -i 1EXR.itp
editconf -f 1EXR.gro -o 1EXR_box.gro -c -d 1.4 -bt cubic
genbox -cp 1EXR_box.gro -cs spc216.gro -o 1EXR_solv.gro -p 1EXR.top -seed 5
grompp -f em.mdp -c 1EXR_solv.gro -p 1EXR.top -o ions.tpr
genion -s ions.tpr -o 1EXR_solv_ions.gro -p 1EXR.top -pname NA+ -nname
CL- -np 17 -seed 66
grompp -f em.mdp -c 1EXR_solv_ions.gro -p 1EXR.top -o em.tpr
mpirun mdrun_d_mpi -v -s em.tpr -x 1EXR_em.xtc -e 1EXR_em.edr -g
1EXR_em.log -c 1EXR_em.gro
grompp -f pr.mdp -c 1EXR_em.gro -p 1EXR.top -o pr.tpr
mpirun mdrun_d_mpi -v -stepout 1000 -s pr.tpr -x 1EXR_pr.xtc -e
1EXR_pr.edr -g 1EXR_pr.log -o 1EXR_pr.trr -c 1EXR_pr.gro
grompp -f md_start.mdp -c 1EXR_pr.gro -p 1EXR.top -o md.tpr
mpirun mdrun_d_mpi -v -stepout 10000 -s md.tpr -x 1EXR_md.xtc -e
1EXR_md.edr -g 1EXR_md.log -o 1EXR_md.trr -c 1EXR_md.gro
The em.mdp:
integrator = steep
maximum number of steps to integrate
nsteps = 50000
;Energy minimizing stuff
emstep = 0.001
emtol = 100.0
; OPTIONS FOR BONDS
constraints = none
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1000
nstvout = 1000
nstfout = 1000
; Output frequency and precision for xtc file
nstxtcout = 1000
xtc-precision = 1000
; Energy monitoring
energygrps = system
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns-type = Grid
; nblist cut-off
rlist = 0.8
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Reaction-Field
rcoulomb = 1.4
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-rf = 62
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Center of mass control
nstcomm = 1000
; Periodic boundary conditions
pbc = xyz
; Mode for center of mass motion removal
comm-mode = linear
; Groups for center of mass motion removal
comm-grps = system
the pr.mdp:
define = -DPOSRES
integrator = md
dt = 0.002 ; ps !
nsteps = 50000 ; total 100ps.
; OPTIONS FOR BONDS
; Constrain control
constraints = all-bonds
; Do not constrain the start configuration
continuation = no
; Type of constraint algorithm
constraint-algorithm = lincs
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100000
nstvout = 100000
nstfout = 100000
; Output frequency and precision for xtc file
nstxtcout = 5000
xtc-precision = 1000
; Energy monitoring
energygrps = Protein Non-protein
nstenergy = 5000
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns-type = Grid
; nblist cut-off
rlist = 0.8
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 62 ; As suggested at J Comput Chem. 2004
Oct;25(13):1656-76.
vdw-type = Cut-off
; cut-off lengths
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = berendsen
; Groups to couple separately, time constant (ps) and reference
temperature (K)
tc-grps = Protein Non-Protein
tau-t = 0.1 0.1
ref-t = 300 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 290K - do not get velocity from gro file.
gen_vel = yes
gen_temp = 290
gen-seed = -1
; Center of mass control
nstcomm = 1000
; Periodic boundary conditions
pbc = xyz
; Mode for center of mass motion removal
comm-mode = Linear
; Groups for center of mass motion removal
comm-grps = system
and the md.mdp:
integrator = md
dt = 0.002 ; ps !
nsteps = 2500000 ; total 5ns.
; OPTIONS FOR BONDS
; Constrain control
constraints = all-bonds
; Do not constrain the start configuration
continuation = no
; Type of constraint algorithm
constraint-algorithm = lincs
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100000
nstvout = 100000
nstfout = 100000
; Output frequency and precision for xtc file
nstxtcout = 5000
xtc-precision = 1000
; Energy monitoring
energygrps = Protein Non-Protein
nstenergy = 1000
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns-type = Grid
; nblist cut-off
rlist = 0.8
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 62 ; As suggested at J Comput Chem. 2004
Oct;25(13):1656-76.
vdw-type = Cut-off
; cut-off lengths
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = berendsen
; Groups to couple separately, time constant (ps) and reference
temperature (K)
tc-grps = Protein Non-Protein
tau-t = 0.1 0.1
ref-t = 300 300
; Pressure coupling
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 290K - do not get velocity from gro file.
gen_vel = yes
gen_temp = 290
gen-seed = -1
; Center of mass control
nstcomm = 10000
; Periodic boundary conditions
pbc = xyz
; Mode for center of mass motion removal
comm-mode = Linear
; Groups for center of mass motion removal
comm-grps = system
The error message we got are LINCS related, eg:
Step 40941, time 40.941 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000021, max 0.000112 (between atoms 981 and 982)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
981 982 34.0 0.0998 0.1000 0.1000
Step 40942, time 40.942 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000140, max 0.001170 (between atoms 981 and 982)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
981 982 31.7 0.1000 0.1001 0.1000
Step 40943, time 40.943 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000106, max 0.000860 (between atoms 981 and 982)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
981 982 30.2 0.1001 0.1001 0.1000
Step 40944, time 40.944 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000053, max 0.000571 (between atoms 979 and 981)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
981 982 35.2 0.1001 0.1000 0.1000
Step 40945, time 40.945 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000225, max 0.001915 (between atoms 981 and 982)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
981 982 36.4 0.1000 0.0998 0.1000
-------------------------------------------------------
Program mdrun_mpi_bg, VERSION 4.5.4
Source code file: ../../../gromacs-4.5.4/src/mdlib/constr.c, line: 176
Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning
threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Now, I think that there is some problem with gromacs 4.5.4 because
the same system, using the same run parameter was successfully
simulated using 4.0.7. I used GROMOS53a6 with SPC water whenever
running this protein. The only difference between a crash and a
successful run was gromacs version.
I'd also add that we need a detailed description of the system,
including force field used and any other special considerations
(distance restraints, modified parameters, etc). An .mdp file would
also be useful for the run that crashes.
The only constraints I had in the system LINCS of all bonds. I didn't
modified the FF in anyway.
Best,
Itamar
-Justin
Do this for 4.0.7 and 4.5.4, for which I trust that you have been
using exactly identical test systems. If not, then please try it
again while conserving the system.
Chris.
-- original message --
Hi Matthew,
Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I
used both GROMACS compiled by me (on my machine) or by the sys-admin on
Linux cluster or blue-gene.
The simulations using 4.5.4 crashed giving LINCS error, which is not the
case with 4.0.7 (using the same mdp and pdb files). Second, I don't thinks
it is poorly compiled bin, as I used both GROMACS compiled with me (on my
machine) or by the sys-admin on Linux cluster/blue-gene.
cheers,
Itamar
On 18 August 2011 01:48, Matthew Zwier <mczwier at gmail.com> wrote:
Could be a system blowing up, or perhaps a mis-compiled binary. What
error messages do you get when the crash occurs?
On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass <itamar.kass at monash.edu>
wrote:
> Hi all GROMACS useres and developers,
>
> I am interesting in simulating a small protein (~140 aa) in water, with
and without Ca ions. In order to do so, I had used version 4.5.4. I had
solvate the protein in water, add ions to naturalise the systems,
equilibrated the systems and then tried productive runs. Now, no
matter what
I did, it crashed after few ps's of free MD or during the PR runs.
>
> Few of the things I had tried are:
> 1. Running the simulations on different systems (OSX, linux or
blue-gene).
> 2. Using single or double precision versions.
> 3. An equilibration stage, 1ns long with a time-step of 1fs, during which
the restrained forces where gradually reduced from 1000 to 50 kJ
mol-1 nm-2.
> 4. Running part of the equilibration stage as NVT and then switched to
NPT.
> 5. Started from different x-ray structures, with resolutions differ from
2.5 to 1.7 Angstrom.
>
> Finally I had moved back to 4.0.7 which worked like charm. I wonder if
someone else had encounter something like this. Attached please
find the mdp
files I used.
>
> All the best,
> Itamar.
>
>
>
>
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