[gmx-users] Simulating Infinite Nanotube
Patrick Lafond
patlafond at gmail.com
Mon Nov 5 17:03:08 CET 2007
Robert,
Thank you for your help, and yes I am absolutely sure that the terminal
carbons are specified as bonded in the topology file. I have used VMD and
done calculations by hand to ensure their distance is correct. I am not
applying any pressure coupling and I have also made sure that the tubes are
sufficiently spaced apart (in the x and y directions). I actually stumbled
upon the gromacs wiki on CNTs (by you) and have made sure to set everything
as you have specified. It is still doing this crumpling though. I have
tried running the simulation without LINCS to get some initial energy
readings and the bond energy of my tube is on the order of 10^7 which is
roughly what it should be if there were bonds that were stretched along the
length of my entire tube rather than simply bonds fromed in the image. It
just doesn't seem as though GROMACS is recognizing the periodic bonds.
Here is part of the log file up until the errors: *NOTE* I have also tried
performing an energy minimization but it results in the exact same output.
I have also gone through the gro file to look at atoms 18, 1495 and 152, 153
both pairs are a perfectly fine distance (roughly 1.421 A) Is there
anything that I am missing? Thank you very much for your help.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
Input Parameters:
integrator = md
nsteps = 1000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 1000
nstlog = 100
nstxout = 100
nstvout = 100
nstfout = 0
nstenergy = 100
nstxtcout = 100
init_t = 0
delta_t = 0.0005
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = full
bUncStart = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = No
epctype = Semiisotropic
tau_p = 4
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
andersen_seed = 815131
rlist = 1
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = EnerPres
fudgeQQ = 0.5
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 2457
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
CPU= 0, lastcg= 1639, targetcg= 820, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 1640
nsb->natoms: 1640
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 1640 1640 1640
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
System total charge: 0.000
Removing pbc first time
Done rmpbc
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 19698.1
There are: 1640 Atoms
Constraining the starting coordinates (step -2)
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
Initializing LINear Constraint Solver
number of constraints is 2460
average number of constraints coupled to one constraint is 4.0
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 15.460966 18 1495 2.822744
After LINCS 3.201852 152 153 0.852419
On 11/1/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
>
> Are you absolutely sure that the terminal carbon atoms are sharing a
> bond in the topology file? Make sure of this. If they really ARE
> bonded within the topology file, then I don't think the crumpling is
> due to Gromacs incorrectly reading the topology (by the way, use
> pbc=full). Provided that the topology file is correct, the crumpling
> may be due to placing the nanotube in a box of wrong dimension. Use
> VMD to visualize the nanotube and its periodic images and make sure
> that the space between images is correct. If the spacing is too small
> or too big, there will be a large amount of stress induced in the tube
> which will lead to crumpling or stretching. Don't apply pressure
> coupling along the axis of the nanotube. In fact, for debugging
> purposes, it might be better to turn off pressure coupling altogether
> until you figure out what's going wrong.
> Bob
>
> On Nov 1, 2007 3:29 PM, Patrick Lafond <patlafond at gmail.com> wrote:
> > Hello, I was wondering if perhaps someone could help me out with running
> a
> > simulation of an infinite CNT. I have searched through the archives
> before
> > and have tried all of the suggestions I was able to find but still can't
> > seem to figure out what the problem is so I decided it best to try and
> ask
> > for direct help. Here is what I have done:
> >
> > 1) Taken the PDB file which is exactly the structure for the tube
> and
> > converted it to a gro file with the proper dimensions for periodic
> height
> > and ample room on the sides.
> > 2) Used x2top to convert the gro file to a topology file using the
> > "-pbc" option. In the topology file I see that it is infact specifying
> > bonds between the carbons at the top of the tube and carbons at the
> bottom
> > of the tube.
> > 3) I have tried running the simulation using different options for
> the
> > pbc in the mdp file. I at first tried pbc = xyz but then changed that
> to
> > full. I also tried fiddling with
> > non-bonded exclusion trying 3, 4, and 5. I also tried changing the time
> > steps to shorter steps.
> > 4) When none of the above mentioned attempts seemed to work I tried
> > making a new slightly shorter tube using the same method mentioned
> above.
> >
> > Regardless of what I seem to do every time the simulation yields
> the
> > same results which is that it won't run. LINCS provides a warning for
> just
> > about every carbon in the tube a handful of times and then reports that
> > there were errors in the simulation. Upon reviewing what it had
> > accomplished the ends of the tube, and 2 rows in the very middle of the
> tube
> > crumple together and them fly apart presumably from how close together
> the
> > atoms are forced there. I have a very strong suspicion that the
> simulation
> > isn't recognizing that the atoms are actually bonded to atoms in the
> image
> > (which would explain the crumpling from how close the atoms are to the
> > periodic image) but cannot figure out how to actually achieve this
> > recognition in the simulation. I read just recently that LINCS has
> problems
> > with molecules containing a lot of bonds but then read the problem is
> more
> > with the constraints applied. It doesn't seem like the error is in
> LINCS
> > rather it is a lack of recognition of bonding between the actual
> molecule
> > and the image. Thanks for your time, I hope I can get some help on
> this.
> >
> > (By the way, I am running the simulation on version 3.1.1 if that might
> > account for any of the problems)
> >
> > Sincerely,
> > Patrick
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071105/0eac902c/attachment.html>
More information about the gromacs.org_gmx-users
mailing list