[gmx-users] Structure optimization failure

[Justin A. Lemkul]

On 6/29/12 6:01 AM, Lara Bunte wrote:
> Hello
>
> I use a CHARMM27 force field and my system is lumiflavin in water. I use the
> spc216 water model, a dodecahedral box with 1.3 nm. I want to make a

CHARMM27 should be combined with TIP3P, not SPC.

> structure minimization. I made a file pr.mdp. Could you please tell me, what
> I could do better in this file, or what is wrong? I guess there has to be
> something wrong, because GROMACS failed with grompp -f pr.mdp -p topol.top -c
> em.gro -o pr.tpr with the error: "Water molecule starting at atom 3924 can
> not be settled. Check for bad contacts and/or reduce the timestep if
> appropriate. "
>
>
> My pr.mdp file is:
>

Your problem is that you're trying to run position-restrained MD, not energy 
minimization.  Consult any tutorial for a more appropriate EM file.  Without 
adequate EM, any simulation with almost certainly crash.

-Justin

>
> title           = lumiflavin NPT equilibration define      = -DPOSRES  ;
> position restrain the protein
>
> ; Run parameters integrator      = md            ; leap-frog integrator
> nsteps          = 50000         ; 2 * 50000 = 100 ps dt              = 0.002
> ; 2 fs
>
> ; Output control nstxout         = 5000          ; save coordinates every 4
> ps nstvout         = 5000          ; save velocities every 4 ps nstenergy
> = 5000          ; save energies every 4 ps nstlog          = 5000          ;
> update log file every 4 ps
>
>
> ; Bond parameters continuation    = yes           ; Restarting after NVT
> 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         = 10             ; edited to 1 rlist           = 1.0
> ; short-range neighborlist cutoff (in nm) rcoulomb        = 1.0           ;
> short-range electrostatic cutoff (in nm) rvdw            = 1.0           ;
> short-range van der Waals cutoff (in nm)
>
> ; Electrostatics coulombtype     = PME           ; Particle Mesh Ewald for
> long-range electrostatics pme_order       = 4             ; cubic
> interpolation fourierspacing  = 0.12          ; grid spacing for FFT
>
> ; Temperature coupling is on tcoupl          = V-rescale     ; modified
> Berendsen thermostat tc-grps         = Isoalloxazin 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 on pcoupl          = berendsen     ; Pressure coupling
> on in NPT pcoupltype      = isotropic     ; uniform scaling of box vectors
> tau_p           = 2.0           ; time constant, in ps ref_p           = 1.0
> ; reference pressure, in bar compressibility = 4.5e-5        ; isothermal
> compressibility of water, bar^-1 refcoord_scaling = all
>
> ; Velocity generation gen_vel     = yes        ; assign velocities from
> Maxwell distribution gen_temp    = 300       ; temperature for Maxwell
> distribution gen_seed    = -1        ; generate a random seed
>
>
> Thank you for helping me 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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