Justin, thanks for your reply. By the way, your GMX tutorials is great!<br><br>I post the gro file and mdp file at the end.<br><br><br><font color="#0000ff"><font size="+3"></font></font><div class="gmail_quote">On Thu, Nov 19, 2009 at 10:09 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><br></div>
Not possible, Gromacs 4.1 hasn't been released :) If you're using version 4.0.1, you shouldn't, because it has a nasty bug that affects performance very severely.</blockquote><div><br>I'm using GMX 4.0.5, not 4.1. Sorry! :)<br>
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I set the box size larger than CNT's length a C-C bond(half up and half down).<br>
If I don't do a EM, it will crumble. But if I do it,it can't satisfy that the box size is larger then CN't length a C-C bond.<br>
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I don't understand this. Are you getting any error messages? Screen and log output are more useful in most cases.<br><div></div></blockquote><div><br>I mean, I make the distance of the top ( or bottom ) C atoms in CNT and the corresponding edge of the box equals the length of a C-C bond( about 0.142nm ).<br>
I use a (16,0) CNT with 832 atoms ( length 5.472nm).I use the following command to produce a CNT-water system<br><br>>editconf -f CNT.pdb -o -box 3.8 3.8 5.614<br><br>No velocities found<br> system size : 1.270 1.270 5.472 (nm)<br>
center : -0.000 0.000 2.736 (nm)<br> box vectors : 0.000 0.000 0.000 (nm)<br> box angles : 0.00 0.00 0.00 (degrees)<br> box volume : 0.00 (nm^3)<br> shift : 1.900 1.900 0.071 (nm)<br>
new center : 1.900 1.900 2.807 (nm)<br>new box vectors : 3.800 3.800 5.614 (nm)<br>new box angles : 90.00 90.00 90.00 (degrees)<br>new box volume : 81.07 (nm^3)<br><br>
>genbox -cp out -cs -p CNT -o b4em.pdb<br><br>Output configuration contains 7513 atoms in 2228 residues<br>Volume : 81.0662 (nm^3)<br>Density : 1026.51 (g/l)<br>Number of SOL molecules: 2227 <br>
<br>Processing topology<br>Adding line for 2227 solvent molecules to topology file (CNT.top)<br><br>>pymol b4em.pdb # I write a python script to remove the SOL molecules in the Carbon nanotube.<br>>editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild the box.<br>
>grompp -v -f em -c b4em -o em -p CNT -maxwarn 5<br>NOTE 1 [file CNT.top, line unknown]:<br> The largest charge group contains 32 atoms.<br> Since atoms only see each other when the centers of geometry of the charge<br>
groups they belong to are within the cut-off distance, too large charge<br> groups can lead to serious cut-off artifacts.<br> For efficiency and accuracy, charge group should consist of a few atoms.<br> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br>
<br><br>Checking consistency between energy and charge groups...<br>Calculating fourier grid dimensions for X Y Z<br>Using a fourier grid of 32x32x48, spacing 0.119 0.119 0.117<br>Estimate for the relative computational load of the PME mesh part: 0.41<br>
This run will generate roughly 15 Mb of data<br>writing run input file...<br><br>There was 1 note<br><br>Back Off! I just backed up em.tpr to ./#em.tpr.1#<br><br>gcq#87: "It's Because Of the Metric System" (Pulp Fiction)<br>
<br>>mdrun -v -s em<br>Back Off! I just backed up md.log to ./#md.log.1#<br>Getting Loaded...<br>Reading file em.tpr, VERSION 4.0.5 (single precision)<br>Loaded with Money<br><br><br>Back Off! I just backed up traj.trr to ./#traj.trr.1#<br>
<br>Back Off! I just backed up traj.xtc to ./#traj.xtc.1#<br><br>Back Off! I just backed up ener.edr to ./#ener.edr.1#<br>starting mdrun 'CNT in water'<br>50000 steps, 25.0 ps.<br>step 0Segmentation fault<br><br>
THE b4em.gro file is like:<br><br>GROtesk MACabre and Sinister<br> 7243<br> 1UNK CX 1 2.508 1.929 0.069<br> 1UNK CX 2 2.496 2.053 0.141<br> 1UNK CX 3 2.460 2.172 0.069<br> 1UNK CX 4 2.401 2.282 0.141<br>
.........................<br>.........................<br> 1UNK CX 828 1.424 1.480 5.541<br> 1UNK CX 829 1.520 1.401 5.469<br> 1UNK CX 830 1.630 1.342 5.541<br> 1UNK CX 831 1.749 1.306 5.469<br>
1UNK CX 832 1.873 1.294 5.541<br> 2SOL OW 833 0.542 1.304 1.163<br> 2SOL HW1 834 0.449 1.297 1.126<br> 2SOL HW2 835 0.553 1.393 1.207<br> 3SOL OW 836 1.716 0.647 0.854<br>
3SOL HW1 837 1.749 0.741 0.854<br> 3SOL HW2 838 1.767 0.593 0.920<br>.........................<br>
.........................<br> 2137SOL OW 7238 0.214 2.438 5.002<br> 2137SOL HW1 7239 0.252 2.379 5.074<br> 2137SOL HW2 7240 0.254 2.412 4.914<br> 2138SOL OW 7241 3.736 2.968 4.022<br>
2138SOL HW1 7242 3.835 2.957 4.013<br> 2138SOL HW2 7243 3.696 2.882 4.054<br> 3.80000 3.80000 5.61400<br><br>The following is my mdp file:<br>; VARIOUS PREPROCESSING OPTIONS<br>title = Yo<br>
cpp = /usr/bin/cpp<br>include = <br>define = <br><br>; RUN CONTROL PARAMETERS<br>integrator = md<br>; Start time and timestep in ps<br>tinit = 0<br>
dt = 0.0005<br>nsteps = 50000<br>; For exact run continuation or redoing part of a run<br>init_step = 0<br>; mode for center of mass motion removal<br>comm-mode = Linear<br>
; number of steps for center of mass motion removal<br>nstcomm = 1<br>; group(s) for center of mass motion removal<br>comm-grps = <br><br>; LANGEVIN DYNAMICS OPTIONS<br>; Temperature, friction coefficient (amu/ps) and random seed<br>
;bd-temp = 300<br>bd-fric = 0<br>ld-seed = 1993<br><br>; OUTPUT CONTROL OPTIONS<br>; Output frequency for coords (x), velocities (v) and forces (f)<br>nstxout = 1000<br>
nstvout = 1000<br>nstfout = 1000<br>; Checkpointing helps you continue after crashes<br>nstcheckpoint = 1000<br>; Output frequency for energies to log file and energy file<br>nstlog = 1000<br>
nstenergy = 1000<br>; Output frequency and precision for xtc file<br>nstxtcout = 1000<br>xtc-precision = 1000<br>; This selects the subset of atoms for the xtc file. You can<br>; select multiple groups. By default all atoms will be written.<br>
xtc-grps = <br>; Selection of energy groups<br>energygrps = <br><br>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency<br>nstlist = 5<br>; ns algorithm (simple or grid)<br>
ns_type = grid<br>; Periodic boundary conditions: xyz (default), no (vacuum)<br>; or full (infinite systems only)<br>pbc = xyz<br>periodic_molecules = yes<br>; nblist cut-off <br>
rlist = 0.9<br>;domain-decomposition = no<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>coulombtype = PME<br>rcoulomb-switch = 0<br>rcoulomb = 0.9<br>
; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>vdw-type = Cut-off<br>; cut-off lengths <br>rvdw-switch = 0<br>
rvdw = 0.95<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>; Extension of the potential lookup tables beyond the cut-off<br>table-extension = 1<br>
; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.12<br>; FFT grid size, when a value is 0 fourierspacing will be used<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>
; EWALD/PME/PPPM parameters<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>epsilon_surface = 0<br>optimize_fft = no<br><br>; GENERALIZED BORN ELECTROSTATICS<br>
; Algorithm for calculating Born radii<br>gb_algorithm = Still<br>; Frequency of calculating the Born radii inside rlist<br>nstgbradii = 1<br>; Cutoff for Born radii calculation; the contribution from atoms<br>
; between rlist and rgbradii is updated every nstlist steps<br>rgbradii = 2<br>; Salt concentration in M for Generalized Born models<br>gb_saltconc = 0<br><br>; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)<br>
implicit_solvent = No<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>; Temperature coupling <br>Tcoupl = v-rescale<br>; Groups to couple separately<br>tc-grps = system<br>; Time constant (ps) and reference temperature (K)<br>
tau_t = 0.1<br>ref_t = 300<br>; Pressure coupling <br>Pcoupl = no<br>Pcoupltype = isotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>
tau_p = 1<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Random seed for Andersen thermostat<br>andersen_seed = 815131<br><br>; SIMULATED ANNEALING <br>; Type of annealing for each temperature group (no/single/periodic)<br>
annealing = no<br>; Number of time points to use for specifying annealing in each group<br>annealing_npoints = <br>; List of times at the annealing points for each group<br>annealing_time = <br>
; Temp. at each annealing point, for each group.<br>annealing_temp = <br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = yes<br>gen_temp = 300<br>gen_seed = 1993<br>
<br>; OPTIONS FOR BONDS <br>constraints = none<br>; Type of constraint algorithm<br>constraint-algorithm = Lincs<br>; Do not constrain the start configuration<br>unconstrained-start = no<br>; Use successive overrelaxation to reduce the number of shake iterations<br>
Shake-SOR = no<br>; Relative tolerance of shake<br>shake-tol = 1e-04<br>; Highest order in the expansion of the constraint coupling matrix<br>lincs-order = 4<br>; Number of iterations in the final step of LINCS. 1 is fine for<br>
; normal simulations, but use 2 to conserve energy in NVE runs.<br>; For energy minimization with constraints it should be 4 to 8.<br>lincs-iter = 1<br>; Lincs will write a warning to the stderr if in one step a bond<br>
; rotates over more degrees than<br>lincs-warnangle = 30<br>; Convert harmonic bonds to morse potentials<br>morse = no<br><br>; ENERGY GROUP EXCLUSIONS<br>; Pairs of energy groups for which all non-bonded interactions are excluded<br>
energygrp_excl = <br><br>; NMR refinement stuff <br>; Distance restraints type: No, Simple or Ensemble<br>disre = No<br>; Force weighting of pairs in one distance restraint: Conservative or Equal<br>
disre-weighting = Conservative<br>; Use sqrt of the time averaged times the instantaneous violation<br>disre-mixed = no<br>disre-fc = 1000<br>disre-tau = 0<br>; Output frequency for pair distances to energy file<br>
nstdisreout = 100<br>; Orientation restraints: No or Yes<br>orire = no<br>; Orientation restraints force constant and tau for time averaging<br>orire-fc = 0<br>orire-tau = 0<br>
orire-fitgrp = <br>; Output frequency for trace(SD) to energy file<br>nstorireout = 100<br>; Dihedral angle restraints: No, Simple or Ensemble<br>dihre = No<br>dihre-fc = 1000<br>
dihre-tau = 0<br>; Output frequency for dihedral values to energy file<br>nstdihreout = 100<br><br><br><br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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I have searched google and gmx mail list, but still can't solve it .<br>
<br>
I found that GMX online document about Carbon Nanotube(<a href="http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube" target="_blank">http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube</a>)<br>
say,<br>
<br>
Be absolutely sure that the "terminal" carbon atoms are sharing a bond in the topology file.<br>
<br>
I don't understand it.How should I do?<br>
<br>
</blockquote>
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Make sure there is a bond in your topology between the appropriate atoms at one "edge" of the box to the appropriate atoms at the other "edge" of the box.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Blog: <a href="http://blog.4message.net" target="_blank">http://blog.4message.net</a><br>