[gmx-users] GROMACS 4.5.4 keep crashing all the time
Itamar Kass
itamar.kass at monash.edu
Thu Aug 18 03:34:58 CEST 2011
Hi Chris,
thanks for the advice, I have to say I tried this as well without any success.
Itamar
On 18/08/2011, at 11:11 AM, chris.neale at utoronto.ca wrote:
> 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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-----
"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.Kass at monash.edu
============================================
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