[gmx-users] Problem with CGMD
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 30 14:58:47 CET 2009
Anirban Ghosh wrote:
> Hi ALL,
>
> Thanks Justin for your reply.
> Now after solvating my CG system of protein in lipid bilayer, I did EM
> and the final energy values were reasonable. But while running MD I am
> getting the following error:
>
> -----------------------------------------------------------------------------------
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed
> -----------------------------------------------------------------------------------
>
> In the archives I found this error and possible solution "to check the
> structure". But that is for all-atom system and according to me my CG
> system is OK. But I am not sure about the mdp parameters that I got from
> a example script from MARTINI site for running lipid MD. So can you
> please check the mdp file and suggest a solution for this problem.
That advice is not specific for atomistic MD. If there is something inherently
wrong with your structure, then you will have problems. I'm curious to know how
you decided that everything was fine, because it certainly is not!
Have you watched the trajectory? Does the crash happen immediately? In my
experience, a dt > 0.02 always crashes when using MARTINI, but I know the
authors claim it can go as high as 0.04.
-Justin
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
> ;
> ; for use with GROMACS 3.3
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS =
> title = Martini
> cpp = /usr/bin/cpp
>
> ; RUN CONTROL PARAMETERS =
> ; MARTINI - Most simulations are stable with dt=40 fs,
> ; some (especially rings) require 20-30 fs.
> ; The range of time steps used for parametrization
> ; is 20-40 fs, using smaller time steps is therefore not recommended.
>
> integrator = md
> ; start time and timestep in ps
> tinit = 0.0
> dt = 0.030
> nsteps = 900000
> ; number of steps for center of mass motion removal =
> nstcomm = 1
> comm-grps =
>
> ; 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 = 1000
> ; Output frequency and precision for xtc file =
> nstxtcout = 1000
> 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 =
>
> ; NEIGHBORSEARCHING PARAMETERS =
> ; MARTINI - no need for more frequent updates
> ; or larger neighborlist cut-off due
> ; to the use of shifted potential energy functions.
>
> ; 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 =
> ; MARTINI - vdw and electrostatic interactions are used
> ; in their shifted forms. Changing to other types of
> ; electrostatics will affect the general performance of
> ; the model.
>
> ; 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 =
> ; MARTINI - normal temperature and pressure coupling schemes
> ; can be used. It is recommended to couple individual groups
> ; in your system seperately.
>
> ; Temperature coupling =
> tcoupl = Berendsen
> ; Groups to couple separately =
> tc-grps = Protein DSPC W
> ; Time constant (ps) and reference temperature (K) =
> tau_t = 0.3 0.3 0.3
> ref_t = 315 315 315
> ; Pressure coupling =
> Pcoupl = berendsen
> Pcoupltype = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> tau_p = 3.0
> compressibility = 3e-5
> ref_p = 1.0
>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel = no
> gen_temp = 315
> gen_seed = 666
>
> ; OPTIONS FOR BONDS =
> ; MARTINI - for ring systems constraints are defined
> ; which are best handled using Lincs.
>
> 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
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Any suggestion is welcome.
>
> Regards,
>
> Anirban
>
>
> ------------------------------------------------------------------------
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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