[gmx-users] minimization problem (Martini simulation)
politr at fh.huji.ac.il
politr at fh.huji.ac.il
Tue Jun 28 00:04:38 CEST 2011
Dear Justin,
Thank you very much for your answer.
Can you please explain me what do you mean by saying "EM wasn't
sufficient". What information do you need in order be able to help?
I run EM with emtol=60 and I got the following energies:
Steepest Descents converged to Fmax < 60 in 2256 steps
Potential Energy = -1.2244622e+07
Maximum force = 4.7755444e+01 on atom 1659
Norm of force = 6.3245118e-01
Everything seems ok.
After that I run MD using mdp file attached and I got the following error:
Started mdrun on node 0 Tue Jun 28 00:10:12 2011
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond G96Angle Improper Dih. LJ (SR) Coulomb (SR)
6.39093e+03 9.79589e+03 3.77765e+02 -1.22386e+07 -1.82773e+03
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-1.22239e+07 1.25745e+00 -1.22239e+07 2.55766e-04 -1.14611e+03
Cons. rmsd ()
4.25390e-06
DD step 9 load imb.: force 3.0%
-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
-------------------------------------------------------
"Step Aside, Butch" (Pulp Fiction)
I found that this error is connected to problems with minimization but
unfortunately I don't know how to fix it.
I will appreciate very much any help.
Thank you.
Regina
mdp file used:
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.030
nsteps = 40000000
; number of steps for center of mass motion removal =
nstcomm = 1
; Groups for center of mass motion removal
comm-grps = System
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 0
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = Protein_PSE W_ION
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = Protein_PSE W_ION
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 300 300
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 5.0 5.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 300
gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>
> politr at fh.huji.ac.il wrote:
>> Dear Gromacs users and developers,
>> I forgot to note that I'm talking about a Martini simulation.
>> I'm trying to set up simulation. I have a big simulation of
>> something like half million CG atoms. The problem is that I have a
>> minimization problem. I'm getting the following error:
>> Converged to machine precision,
>> but not to the requested precision Fmax < 10
>
> This is not really an error:
>
> http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision
>
> The success of any subsequent MD depends on the magnitude of the
> maximum force the EM procedure achieved. Minimizing to such a low
> force is very difficult and may not be possible for all systems.
>
>> I tried to use a bigger emtol(emtol=20) and it still didn't
>> converge.However I still run the MD with dt = 0.03 and nstxout = 1.
>> after something like 100 steps the system blow up.
>
> Perhaps your EM wasn't sufficient, but based on the information
> you've posted, it's hard to draw any real conclusion about that.
>
>> I will appreciate any help with this issue.
>> Many thanks in advance.
>> P.S May it help if I minimize a smaller system and replicate it
>> after that. How exactly can I do replication?
>
> It may or may not help, but I don't think it likely. You can always
> try it and see. Certainly minimizing a smaller system will give you
> a faster result. You can replicate any unit cell in any dimension
> using genconf -nbox.
>
> -Justin
>
> --
> ========================================
>
> 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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