[gmx-users] Problems in mdrun - CHARMM27

[Justin Lemkul]

On 9/20/12 3:04 PM, Lara Bunte wrote:
> Hello
>
> Could you please take a look on my new pr.mdp file that I created for equilibrating water around lumiflavin. grompp works but I guess there must be something wrong because after grompp I am using mdrun and get this warning:
>
> Warning: 1-4 interaction between 1 and 5 at distance 2.429 which is larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
>
> step 1: Water molecule starting at atom 8655 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
>
> My system is lumiflavin in a dodecahedron box, a tip3p water model and the CHARMM27 force field. This is my pr.mdp file:
>

You are not using correct settings.  Peter posted these the other day for CHARMM27:

http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html

Beyond that, how successful was energy minimization?  How did you derive the 
topology?  Does an in vacuo run of just the solute work, or does it fail as well 
(implicates an incorrect topology)?

-Justin

> title           = Lumiflavin NVT equilibration
> define          = -DPOSRES
> ; Run parameters
> integrator      = md
> nsteps          = 50000        ; 2 * 50000 = 100 ps
> dt              = 0.002            ; 2 fs
> ; Output control
> nstxout         = 100           ; save coordinates every 0.2 ps
> nstvout         = 100           ; save velocities every 0.2 ps
> nstenergy       = 100          ; save energies every 0.2 ps
> nstlog          = 100            ; update log file every 0.2 ps
> ; Bond parameters
> continuation    = no            ; first dynamics run
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cells
> nstlist         = 5                ; 10 fs
> rlist           = 1.2               ; short-range neighborlist cutoff (in nm)
> rlistlong       = 1.4
> rcoulomb        = 1.2         ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME      ; Particle Mesh Ewald for long-range electrostatics
> pme_order       = 4             ; cubic interpolation
> fourierspacing  = 0.16        ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = ISO SOL       ; two coupling groups - more accurate
> tau_t           = 0.1   0.1     ; time constant, in ps
> ref_t           = 300   300     ; reference temperature, one for each group, in K
> ; Pressure coupling is off
> pcoupl          = no            ; no pressure coupling in NVT
> ; Velocity generation
> gen_vel         = yes           ; assign velocities from Maxwell distribution
> gen_temp        = 300           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
>
> Thanks for helping me
>
> Best greetings
> Lara
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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