Robert,<br><br>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.
<br><br>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.<br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
<br>Berendsen<br>GROMACS: Fast, Flexible and Free<br>J. Comp. Chem. 26 (2005) pp. 1701-1719<br>-------- -------- --- Thank You --- -------- --------<br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>E. Lindahl and B. Hess and D. van der Spoel
<br>GROMACS 3.0: A package for molecular simulation and trajectory analysis<br>J. Mol. Mod. 7 (2001) pp. 306-317<br>-------- -------- --- Thank You --- -------- --------<br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
<br>H. J. C. Berendsen, D. van der Spoel and R. van Drunen<br>GROMACS: A message-passing parallel molecular dynamics implementation<br>Comp. Phys. Comm. 91 (1995) pp. 43-56<br>-------- -------- --- Thank You --- -------- --------
<br><br>Input Parameters:<br> integrator = md<br> nsteps = 1000<br> init_step = 0<br> ns_type = Grid<br> nstlist = 10<br> ndelta = 2<br>
bDomDecomp = FALSE<br> decomp_dir = 0<br> nstcomm = 1<br> comm_mode = Linear<br> nstcheckpoint = 1000<br> nstlog = 100<br> nstxout = 100
<br> nstvout = 100<br> nstfout = 0<br> nstenergy = 100<br> nstxtcout = 100<br> init_t = 0<br> delta_t = 0.0005<br> xtcprec = 1000
<br> nkx = 0<br> nky = 0<br> nkz = 0<br> pme_order = 4<br> ewald_rtol = 1e-05<br> ewald_geometry = 0<br> epsilon_surface = 0
<br> optimize_fft = TRUE<br> ePBC = full<br> bUncStart = FALSE<br> bShakeSOR = FALSE<br> etc = Berendsen<br> epc = No<br> epctype = Semiisotropic
<br> tau_p = 4<br> ref_p (3x3):<br> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 2]={ 0.00000e+00, 0.00000e+00
, 0.00000e+00}<br> compress (3x3):<br> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> compress[ 2]={ 0.00000e+00, 0.00000e+00
, 0.00000e+00}<br> andersen_seed = 815131<br> rlist = 1<br> coulombtype = Cut-off<br> rcoulomb_switch = 0<br> rcoulomb = 1<br> vdwtype = Cut-off<br>
rvdw_switch = 0<br> rvdw = 1<br> epsilon_r = 1<br> epsilon_rf = 1<br> tabext = 1<br> gb_algorithm = Still<br> nstgbradii = 1<br>
rgbradii = 2<br> gb_saltconc = 0<br> implicit_solvent = No<br> DispCorr = EnerPres<br> fudgeQQ = 0.5<br> free_energy = no<br> init_lambda = 0
<br> sc_alpha = 0<br> sc_power = 0<br> sc_sigma = 0.3<br> delta_lambda = 0<br> disre_weighting = Conservative<br> disre_mixed = FALSE<br> dr_fc = 1000
<br> dr_tau = 0<br> nstdisreout = 100<br> orires_fc = 0<br> orires_tau = 0<br> nstorireout = 100<br> dihre-fc = 1000<br> dihre-tau = 0
<br> nstdihreout = 100<br> em_stepsize = 0.01<br> em_tol = 10<br> niter = 20<br> fc_stepsize = 0<br> nstcgsteep = 1000<br> nbfgscorr = 10
<br> ConstAlg = Lincs<br> shake_tol = 1e-04<br> lincs_order = 4<br> lincs_warnangle = 30<br> lincs_iter = 1<br> bd_fric = 0<br> ld_seed = 1993
<br> cos_accel = 0<br> deform (3x3):<br> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 2]={ 0.00000e+00,
0.00000e+00, 0.00000e+00}<br> userint1 = 0<br> userint2 = 0<br> userint3 = 0<br> userint4 = 0<br> userreal1 = 0<br> userreal2 = 0<br> userreal3 = 0
<br> userreal4 = 0<br>grpopts:<br> nrdf: 2457<br> ref_t: 300<br> tau_t: 0.1<br>anneal: No<br>ann_npoints: 0<br> acc: 0 0 0
<br> nfreeze: N N N<br> energygrp_flags[ 0]: 0<br> efield-x:<br> n = 0<br> efield-xt:<br> n = 0<br> efield-y:<br> n = 0<br> efield-yt:<br> n = 0<br> efield-z:
<br> n = 0<br> efield-zt:<br> n = 0<br> bQMMM = FALSE<br> QMconstraints = 0<br> QMMMscheme = 0<br> scalefactor = 1<br>qm_opts:<br> ngQM = 0<br>
CPU= 0, lastcg= 1639, targetcg= 820, myshift= 0<br>nsb->shift = 1, nsb->bshift= 0<br>Neighbor Search Blocks<br>nsb->nodeid: 0<br>nsb->nnodes: 1<br>nsb->cgtotal: 1640<br>nsb->natoms: 1640
<br>nsb->shift: 1<br>nsb->bshift: 0<br>Nodeid index homenr cgload workload<br> 0 0 1640 1640 1640<br><br>Table routines are used for coulomb: FALSE<br>Table routines are used for vdw: FALSE
<br>Cut-off's: NS: 1 Coulomb: 1 LJ: 1<br>System total charge: 0.000<br>Removing pbc first time<br>Done rmpbc<br>Center of mass motion removal mode is Linear<br>We have the following groups for center of mass motion removal:
<br> 0: rest, initial mass: 19698.1<br>There are: 1640 Atoms<br><br>Constraining the starting coordinates (step -2)<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
<br>Molecular dynamics with coupling to an external bath<br>J. Chem. Phys. 81 (1984) pp. 3684-3690<br>-------- -------- --- Thank You --- -------- --------<br><br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
<br>B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije<br>LINCS: A Linear Constraint Solver for molecular simulations<br>J. Comp. Chem. 18 (1997) pp. 1463-1472<br>-------- -------- --- Thank You --- -------- --------
<br><br><br>Initializing LINear Constraint Solver<br> number of constraints is 2460<br> average number of constraints coupled to one constraint is 4.0<br><br> Rel. Constraint Deviation: Max between atoms RMS<br>
Before LINCS 15.460966 18 1495 2.822744<br> After LINCS 3.201852 152 153 0.852419<br><br><br><br><div><span class="gmail_quote">On 11/1/07, <b class="gmail_sendername">Robert Johnson
</b> <<a href="mailto:bobjohnson1981@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">bobjohnson1981@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Are you absolutely sure that the terminal carbon atoms are sharing a<br>bond in the topology file? Make sure of this. If they really ARE<br>bonded within the topology file, then I don't think the crumpling is<br>due to Gromacs incorrectly reading the topology (by the way, use
<br>pbc=full). Provided that the topology file is correct, the crumpling<br>may be due to placing the nanotube in a box of wrong dimension. Use<br>VMD to visualize the nanotube and its periodic images and make sure<br>that the space between images is correct. If the spacing is too small
<br>or too big, there will be a large amount of stress induced in the tube<br>which will lead to crumpling or stretching. Don't apply pressure<br>coupling along the axis of the nanotube. In fact, for debugging<br>purposes, it might be better to turn off pressure coupling altogether
<br>until you figure out what's going wrong.<br>Bob<br><br>On Nov 1, 2007 3:29 PM, Patrick Lafond <<a href="mailto:patlafond@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">patlafond@gmail.com
</a>> wrote:<br>> Hello, I was wondering if perhaps someone could help me out with running a
<br>> simulation of an infinite CNT. I have searched through the archives before<br>> and have tried all of the suggestions I was able to find but still can't<br>> seem to figure out what the problem is so I decided it best to try and ask
<br>> for direct help. Here is what I have done:<br>><br>> 1) Taken the PDB file which is exactly the structure for the tube and<br>> converted it to a gro file with the proper dimensions for periodic height
<br>> and ample room on the sides.<br>> 2) Used x2top to convert the gro file to a topology file using the<br>> "-pbc" option. In the topology file I see that it is infact specifying<br>> bonds between the carbons at the top of the tube and carbons at the bottom
<br>> of the tube.<br>> 3) I have tried running the simulation using different options for the<br>> pbc in the mdp file. I at first tried pbc = xyz but then changed that to<br>> full. I also tried fiddling with
<br>> non-bonded exclusion trying 3, 4, and 5. I also tried changing the time<br>> steps to shorter steps.<br>> 4) When none of the above mentioned attempts seemed to work I tried<br>> making a new slightly shorter tube using the same method mentioned above.
<br>><br>> Regardless of what I seem to do every time the simulation yields the<br>> same results which is that it won't run. LINCS provides a warning for just<br>> about every carbon in the tube a handful of times and then reports that
<br>> there were errors in the simulation. Upon reviewing what it had<br>> accomplished the ends of the tube, and 2 rows in the very middle of the tube<br>> crumple together and them fly apart presumably from how close together the
<br>> atoms are forced there. I have a very strong suspicion that the simulation<br>> isn't recognizing that the atoms are actually bonded to atoms in the image<br>> (which would explain the crumpling from how close the atoms are to the
<br>> periodic image) but cannot figure out how to actually achieve this<br>> recognition in the simulation. I read just recently that LINCS has problems<br>> with molecules containing a lot of bonds but then read the problem is more
<br>> with the constraints applied. It doesn't seem like the error is in LINCS<br>> rather it is a lack of recognition of bonding between the actual molecule<br>> and the image. Thanks for your time, I hope I can get some help on this.
<br>><br>> (By the way, I am running the simulation on version 3.1.1 if that might<br>> account for any of the problems)<br>><br>> Sincerely,<br>> Patrick<br>><br>> _______________________________________________
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