[gmx-users] Erro in SMD simulation..

[Justin Lemkul]

On 4/1/14, 6:16 AM, Kalyanashis wrote:
> Dear all,
>      I am trying to run an SMD simulation of an enzyme system with a drug
> molecule. The final SMD run was crashed at the middle of the MD run(crashed
> at 1370 ps). I got an error and the erro is
> " Fatal error:
> Distance of pull group 1 (8.662854 nm) is larger than 0.49 times the box
> size (8.832091)"
> I have checked for the solution in the gromacs user
> forum(http://gromacs.5086.x6.nabble.com/Distance-of-pull-group-1-2-142226-nm-is-larger-than-0-49-times-the-box-size-2-184750-td5007938.html#a5007939,
> http://gromacs.5086.x6.nabble.com/Pull-code-with-pull-geometry-cylinder-generates-error-Distance-of-pull-group-1-4-030185-nm-is-larger-td5001603.html#a5001695)
> but I did get any information.
> I have attache my smd.mdp file
> title                  =  2JEY-HI6
> cpp                    =  /usr/bin/cpp
> constraints            =  all-bonds
> integrator             =  md
> dt                     =  0.001 ; ps !
> nsteps                 =  5000000 ; total 2 ns.
> nstcomm                =  100
> nstxout                =  500; collect data every 1 ps
> ;nstxtcout              =  500
> ;xtc_precision          =  1000
> nstvout                =  1000
> nstfout                =  0
> nstenergy              =  100
> nstlog                 =  100
> nstlist                =  100
> ns_type                =  grid
> pbc                   =  xyz
> rlist                  =  1.0
> coulombtype            =  PME
> rcoulomb               =  1.0
> vdwtype                =  cutoff
> rvdw                   =  1.4
> fourierspacing         =  0.12
> fourier_nx             =  0
> fourier_ny             =  0
> fourier_nz             =  0
> pme_order              =  4
> ewald_rtol             =  1e-5
> optimize_fft           =  yes
> ; Berendsen temperature coupling is on
> Tcoupl              =  berendsen
> tau_t               =  0.5
> tcgrps              =  system
> ref_t               =  300
> ; Pressure coupling is on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic ; Use semiisotropic when working with
> membranes
> tau_p               =  2.0
> compressibility     =  4.5e-5
> ref_p               =  1.0
> refcoord-scaling    =  all
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
> ;COM pulling
> pull                     = umbrella
> pull_geometry            = distance
> pull_dim                 = N N Y
> pull_r1                  = 1
> pull_r0                  = 1
> ;pull_constr_tot          = 1e-6
> pull_start               = yes
> pull_nstxout             = 10
> pull_nstfout             = 1
> pull_ngroups             = 1
> ;name of reference group
> pull_group0              = Protein
> ;pull_weights             = 0
> ;name of pull group
> pull_group1              = UNK
> ;pull_weights             = 0
> pull_vec1                = 0.0 0.0 -1
> ;ref. distance at t=0
> ;pull_init1               = -2.4477384   -1.0229216   -1.5900776
> ;rate of change of ref. gr. [nm/ps]
> pull_rate1               = 0.0005
> ;force constant [KJ mol^-1 nm^-2]
> pull_k1                  = 1586.747
> ;pull_kB1                =
>
> I changed the pull_k1, added pbc=xyz but nothing is working. One of friend
> got same problem but pbc=xyz was working for his system.
> Please suggest me any probable solution.
>

Your box is too small to pull as far as you have.  With the "distance" geometry, 
the vector between the pulled and reference groups must always be less than half 
the shortest box vector among those used for pulling (in your case, just z).

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

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
http://mackerell.umaryland.edu/~jalemkul

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