[gmx-users] Erro in SMD simulation..
Kalyanashis
kalyan.chem.in at gmail.com
Tue Apr 1 18:57:03 CEST 2014
Thank you Justin for your valuable reply. But you know, my box size is
17.744*17.744*17.744 nm^3. I have used "editconf -bt cubic -f
20-SCH-edit1.pdb -o 20-SCH-edit2.pdb -c -d 1.6" to generate the box. And
the full description of the box size I have used is
"Read 15484 atoms
No velocities found
system size : 7.604 8.101 13.546 (nm)
diameter : 14.544 (nm)
center : 2.405 3.212 -2.870 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
shift : 6.467 5.661 11.742 (nm)
new center : 8.872 8.872 8.872 (nm)
new box vectors : 17.744 17.744 17.744 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume :5587.13 (nm^3)"
Please suggest me the better option for my system. Should I increase the d
value? Actually, the whole system contains approximately 193000 atoms and
whenever I am increasing the d value the atoms no. is increasing
significantly. Is there any option which can allow me to increase the box
size without increasing the number of solvent molecules? And one more more
thing, is the cubic option fine?
Thanks,
Kalyan.
On Tue, Apr 1, 2014 at 7:06 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5015544h51 at n6.nabble.com> wrote:
>
>
> 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
>
> [hidden email] <http://user/SendEmail.jtp?type=node&node=5015544&i=0> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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--
Kalyanashis Jana
email: kalyan.chem.in at gmail.com
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