Hi Chris and Justin,
On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote:
>
>
> chris.ne...@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.
>>> >
>>> >
>>> >
>>> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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-----
"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu
============================================
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