[gmx-users] Regarding error in NPT SIMULATION in VACUM

[David van der Spoel]

On 2014-08-20 17:03, vidhya sankar wrote:
> Dear Justin Thank you for your previous reply
>                                                                       When I run NPT equlibiriation for My CNT CNCASSED CYCLICPETIDE in VACUM
> I have Got the Following error after 3 lacs steps out of 10 lacs
>

What do you *think* will happen when you do pressure coupling in vacuum?

> The X-size of the box (7.750338) times the triclinic skew factor (1.000000) is smaller than the number of DD cells (8) times the smallest allowed cell size (0.969134)
>
> My Box size is 10.83680  10.88700  10.19300
> MY NPT parameters are
> title        = NPT Equilibration for KALP15-DPPC
> define        = -DPOSRES   ; position restrain the protein
> ; Run parameters
> integrator    = md        ; leap-frog integrator
> nsteps        = 1000000    ; 2 * 500000 = 1000 ps (1 ns)
> 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    = 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 cels
> nstlist        = 5            ; 10 fs
> rlist        = 0.9        ; short-range neighborlist cutoff (in nm)
> rcoulomb    = 0.9        ; short-range electrostatic cutoff (in nm)
> rvdw        = 1.4        ; 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        = Nose-Hoover            ; More accurate thermostat
> tc-grps        = Protein CNT    CL    ; three coupling groups - more accurate
> tau_t        = 0.5      0.5    0.5            ; time constant, in ps
> ref_t        = 323       323    323            ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl        = Parrinello-Rahman        ; Pressure coupling on in NPT
> pcoupltype    = isotropic            ; uniform scaling of x-y box vectors, independent z
> tau_p        = 5.0                    ; time constant, in ps
> ref_p        = 1.0    1.0                ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5    4.5e-5    ; isothermal compressibility, bar^-1
> ; Periodic boundary conditions
> pbc            = xyz        ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel        = no        ; Velocity generation is off
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the solvent/ions
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = CNT_protein  CL
> ; Scale COM of reference coordinates
> refcoord_scaling = com
>
> How to Solve this error?
>   Please Help me Which Parameter Shoul I Cahnge in . mdp file?
>
> Thanks in Advance
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se