[gmx-users] Re: Multiple LINCS Warnings in NVT Equillibration

[Justin Lemkul]

On 7/10/13 3:13 AM, ashish24294 wrote:
> I changed the cut-offs as follows, still isn't helping. I tried restraining
> the urea which also didn't work.  I have attached the topology as well.
> topolurea.top
> <http://gromacs.5086.x6.nabble.com/file/n5009723/topolurea.top>
>

The urea.itp looks suspicious to me - there are no angles defined.  There is no 
citation for the parameters in the .itp, so it's hard to validate where they 
came from.  In any case, given the frequency of output you have specified below, 
it should be very useful to watch the trajectory to see what is going wrong. 
Right around 25 ps, you have large oscillations in LJ(SR) and the temperature, 
indicating to me that there is some really nasty geometry emerging that is 
causing velocities to go haywire and the thermostat can't keep up.  Then you get 
the crash.

-Justin

> *The nvt.mdp*
>
> title       = UREA_in_WATER NVT equillibration
> ;define = -DPOSRES_UREA
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> 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
> energygrps  = URE
> ; 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       = 1.0      ; 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  = 0.16      ; grid spacing for FFT
> ; Temperature coupling
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = URE_Water    ; two coupling groups - more accurate
> tau_t       = 0.1   			              ; time constant, in ps
> ref_t       = 300                  ; reference temperature, one for each
> group, in K
> ; Pressure coupling
> pcoupl      = no        ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc         = xyz       ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = yes       ; assign velocities from Maxwell distribution
> gen_temp    = 300       ; temperature for Maxwell distribution
> gen_seed    = -1        ; generate a random seed
>
> Using the above nvt.mdp file i got the attached nvt.log   nvt.log
> <http://gromacs.5086.x6.nabble.com/file/n5009723/nvt.log>
>
>
>
> --
> View this message in context: http://gromacs.5086.x6.nabble.com/Multiple-LINCS-Warnings-in-NVT-Equillibration-tp5009701p5009723.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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