Dear Justin, The grompp doesn't show any fatal error. Using gmxdump I have checked the topol.tpr file, and I found that C6 and C12 parameters of LJ have there completely different values in contrast to those I wrote in silver.itp! Maybe it is the reason. But I wrote parameters in *.itp in units of [E]=kJ/mol and [r]=nm. The C6 and C12 constants were taken from experimental data of bulk silver (from lattice constant and enthalpy of formation), so they must be right. Concerning AMBER03 force field, I am new in MD and I do not know exactly how to check the validation of LJ parameters applying it.
Alex On Fri, Jan 11, 2013 at 12:32 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/11/13 5:02 AM, Alexej Mazheika wrote: > >> Hello >> >> I removed PBC and set space conditions as you recommended. I also modified >> a bit the grompp.mdp (new version is below). However, it did not help to >> prevent the scattering of silver atoms in all directions. The change of >> parameters in LJ doesn't influence on the final geometry. It seems, that >> LJ >> coefficients don't play any role at all! The decrease of the temperature >> (from 300 to 100K) provides only smaller radius of the cloud of flown >> apart >> Ag-atoms. So no Ag125 particle exists at the end. It looks like it doesn't >> recognise the silver.itp with atom parameters, which I designated in >> topol.top. >> >> > If that were true, you would have gotten a fatal error when running > grompp. You can always validate the contents of the .tpr file using > gmxdump to prove to yourself that all the correct information is there. Do > you have sufficient evidence to suggest that those parameters should indeed > stabilize the cluster of silver atoms? Have these parameters been > validated and determined to be appropriate for use with the (biomolecular) > AMBER03 force field? > > -Justin > > *grompp.mdp*: >> >> >> title = Yo >> cpp = /usr/bin/cpp >> >> integrator = md >> tinit = 0 >> dt = 0.002 >> nsteps = 10000 >> init_step = 0 >> comm-mode = ANGULAR >> nstcomm = 1 >> >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstcheckpoint = 1000 >> nstlog = 50 >> nstenergy = 50 >> nstxtcout = 50 >> xtc-precision = 1000 >> >> nstlist = 0 >> ns_type = grid >> pbc = no >> rlist = 0 >> domain-decomposition = no >> >> coulombtype = Cut-off >> rcoulomb-switch = 0 >> rcoulomb = 0 >> epsilon-r = 1 >> vdw-type = Cut-off >> rvdw-switch = 0 >> rvdw = 0 >> >> Tcoupl = v-rescale >> tc-grps = System >> tau_t = 0.1 >> ref_t = 300 >> ld-seed = 1993 >> Pcoupl = no >> andersen_seed = 815131 >> >> annealing = no >> >> gen_vel = yes >> gen_temp = 1 >> gen_seed = 1993 >> constraints = none >> morse = no >> >> >> On Thu, Jan 10, 2013 at 4:40 PM, Justin Lemkul <[email protected]> wrote: >> >> >>> >>> On 1/10/13 6:14 AM, Alexej Mazheika wrote: >>> >>> Hi all! >>>> >>>> I am new in MD and in Gromacs. I try to calculate the structure of an >>>> Ag125 >>>> particle in the gas phase. But during the optimization, all silver atoms >>>> fly apart around the cell. So no cluster exists at the end even by >>>> relatively low temperatures. The constants for LJ potential I took from >>>> experimental data. I guess that something can be wrong in the >>>> grompp.mdp, >>>> which I took from examples in share/tutor/ and modified a bit, but I >>>> cann't >>>> understand what's the matter. Input files are shown below >>>> >>>> Alex >>>> >>>> *conf.gro:* >>>> >>>> >>>> Bulk silver, t = 0.0 >>>> 125 >>>> 0001Clust Ag 1 0.000 0.000 0.000 >>>> 0002Clust Ag 2 0.204 0.204 0.000 >>>> 0003Clust Ag 3 0.409 0.409 0.000 >>>> 0004Clust Ag 4 -0.409 -0.409 0.000 >>>> 0005Clust Ag 5 -0.204 -0.204 0.000 >>>> 0006Clust Ag 6 0.204 0.000 0.204 >>>> 0007Clust Ag 7 0.409 0.204 0.204 >>>> 0008Clust Ag 8 0.613 0.409 0.204 >>>> 0009Clust Ag 9 -0.204 -0.409 0.204 >>>> 0010Clust Ag 10 0.000 -0.204 0.204 >>>> 0011Clust Ag 11 0.409 0.000 0.409 >>>> 0012Clust Ag 12 0.613 0.204 0.409 >>>> 0013Clust Ag 13 0.817 0.409 0.409 >>>> 0014Clust Ag 14 0.000 -0.409 0.409 >>>> 0015Clust Ag 15 0.204 -0.204 0.409 >>>> 0016Clust Ag 16 -0.409 0.000 -0.409 >>>> 0017Clust Ag 17 -0.204 0.204 -0.409 >>>> 0018Clust Ag 18 0.000 0.409 -0.409 >>>> 0019Clust Ag 19 -0.817 -0.409 -0.409 >>>> 0020Clust Ag 20 -0.613 -0.204 -0.409 >>>> 0021Clust Ag 21 -0.204 0.000 -0.204 >>>> 0022Clust Ag 22 0.000 0.204 -0.204 >>>> 0023Clust Ag 23 0.204 0.409 -0.204 >>>> 0024Clust Ag 24 -0.613 -0.409 -0.204 >>>> 0025Clust Ag 25 -0.409 -0.204 -0.204 >>>> 0026Clust Ag 26 0.000 0.204 0.204 >>>> 0027Clust Ag 27 0.204 0.409 0.204 >>>> 0028Clust Ag 28 0.409 0.613 0.204 >>>> 0029Clust Ag 29 -0.409 -0.204 0.204 >>>> 0030Clust Ag 30 -0.204 0.000 0.204 >>>> 0031Clust Ag 31 0.204 0.204 0.409 >>>> 0032Clust Ag 32 0.409 0.409 0.409 >>>> 0033Clust Ag 33 0.613 0.613 0.409 >>>> 0034Clust Ag 34 -0.204 -0.204 0.409 >>>> 0035Clust Ag 35 0.000 0.000 0.409 >>>> 0036Clust Ag 36 0.409 0.204 0.613 >>>> 0037Clust Ag 37 0.613 0.409 0.613 >>>> 0038Clust Ag 38 0.817 0.613 0.613 >>>> 0039Clust Ag 39 0.000 -0.204 0.613 >>>> 0040Clust Ag 40 0.204 0.000 0.613 >>>> 0041Clust Ag 41 -0.409 0.204 -0.204 >>>> 0042Clust Ag 42 -0.204 0.409 -0.204 >>>> 0043Clust Ag 43 0.000 0.613 -0.204 >>>> 0044Clust Ag 44 -0.817 -0.204 -0.204 >>>> 0045Clust Ag 45 -0.613 0.000 -0.204 >>>> 0046Clust Ag 46 -0.204 0.204 0.000 >>>> 0047Clust Ag 47 0.000 0.409 0.000 >>>> 0048Clust Ag 48 0.204 0.613 0.000 >>>> 0049Clust Ag 49 -0.613 -0.204 0.000 >>>> 0050Clust Ag 50 -0.409 0.000 0.000 >>>> 0051Clust Ag 51 0.000 0.409 0.409 >>>> 0052Clust Ag 52 0.204 0.613 0.409 >>>> 0053Clust Ag 53 0.409 0.817 0.409 >>>> 0054Clust Ag 54 -0.409 0.000 0.409 >>>> 0055Clust Ag 55 -0.204 0.204 0.409 >>>> 0056Clust Ag 56 0.204 0.409 0.613 >>>> 0057Clust Ag 57 0.409 0.613 0.613 >>>> 0058Clust Ag 58 0.613 0.817 0.613 >>>> 0059Clust Ag 59 -0.204 0.000 0.613 >>>> 0060Clust Ag 60 0.000 0.204 0.613 >>>> 0061Clust Ag 61 0.409 0.409 0.817 >>>> 0062Clust Ag 62 0.613 0.613 0.817 >>>> 0063Clust Ag 63 0.817 0.817 0.817 >>>> 0064Clust Ag 64 0.000 0.000 0.817 >>>> 0065Clust Ag 65 0.204 0.204 0.817 >>>> 0066Clust Ag 66 -0.409 0.409 0.000 >>>> 0067Clust Ag 67 -0.204 0.613 0.000 >>>> 0068Clust Ag 68 0.000 0.817 0.000 >>>> 0069Clust Ag 69 -0.817 0.000 0.000 >>>> 0070Clust Ag 70 -0.613 0.204 0.000 >>>> 0071Clust Ag 71 -0.204 0.409 0.204 >>>> 0072Clust Ag 72 0.000 0.613 0.204 >>>> 0073Clust Ag 73 0.204 0.817 0.204 >>>> 0074Clust Ag 74 -0.613 0.000 0.204 >>>> 0075Clust Ag 75 -0.409 0.204 0.204 >>>> 0076Clust Ag 76 0.000 -0.409 -0.409 >>>> 0077Clust Ag 77 0.204 -0.204 -0.409 >>>> 0078Clust Ag 78 0.409 0.000 -0.409 >>>> 0079Clust Ag 79 -0.409 -0.817 -0.409 >>>> 0080Clust Ag 80 -0.204 -0.613 -0.409 >>>> 0081Clust Ag 81 0.204 -0.409 -0.204 >>>> 0082Clust Ag 82 0.409 -0.204 -0.204 >>>> 0083Clust Ag 83 0.613 0.000 -0.204 >>>> 0084Clust Ag 84 -0.204 -0.817 -0.204 >>>> 0085Clust Ag 85 0.000 -0.613 -0.204 >>>> 0086Clust Ag 86 0.409 -0.409 0.000 >>>> 0087Clust Ag 87 0.613 -0.204 0.000 >>>> 0088Clust Ag 88 0.817 0.000 0.000 >>>> 0089Clust Ag 89 0.000 -0.817 0.000 >>>> 0090Clust Ag 90 0.204 -0.613 0.000 >>>> 0091Clust Ag 91 -0.409 -0.409 -0.817 >>>> 0092Clust Ag 92 -0.204 -0.204 -0.817 >>>> 0093Clust Ag 93 0.000 0.000 -0.817 >>>> 0094Clust Ag 94 -0.817 -0.817 -0.817 >>>> 0095Clust Ag 95 -0.613 -0.613 -0.817 >>>> 0096Clust Ag 96 -0.204 -0.409 -0.613 >>>> 0097Clust Ag 97 0.000 -0.204 -0.613 >>>> 0098Clust Ag 98 0.204 0.000 -0.613 >>>> 0099Clust Ag 99 -0.613 -0.817 -0.613 >>>> 0100Clust Ag 100 -0.409 -0.613 -0.613 >>>> 0101Clust Ag 101 0.000 -0.204 -0.204 >>>> 0102Clust Ag 102 0.204 0.000 -0.204 >>>> 0103Clust Ag 103 0.409 0.204 -0.204 >>>> 0104Clust Ag 104 -0.409 -0.613 -0.204 >>>> 0105Clust Ag 105 -0.204 -0.409 -0.204 >>>> 0106Clust Ag 106 0.204 -0.204 0.000 >>>> 0107Clust Ag 107 0.409 0.000 0.000 >>>> 0108Clust Ag 108 0.613 0.204 0.000 >>>> 0109Clust Ag 109 -0.204 -0.613 0.000 >>>> 0110Clust Ag 110 0.000 -0.409 0.000 >>>> 0111Clust Ag 111 0.409 -0.204 0.204 >>>> 0112Clust Ag 112 0.613 0.000 0.204 >>>> 0113Clust Ag 113 0.817 0.204 0.204 >>>> 0114Clust Ag 114 0.000 -0.613 0.204 >>>> 0115Clust Ag 115 0.204 -0.409 0.204 >>>> 0116Clust Ag 116 -0.409 -0.204 -0.613 >>>> 0117Clust Ag 117 -0.204 0.000 -0.613 >>>> 0118Clust Ag 118 0.000 0.204 -0.613 >>>> 0119Clust Ag 119 -0.817 -0.613 -0.613 >>>> 0120Clust Ag 120 -0.613 -0.409 -0.613 >>>> 0121Clust Ag 121 -0.204 -0.204 -0.409 >>>> 0122Clust Ag 122 0.000 0.000 -0.409 >>>> 0123Clust Ag 123 0.204 0.204 -0.409 >>>> 0124Clust Ag 124 -0.613 -0.613 -0.409 >>>> 0125Clust Ag 125 -0.409 -0.409 -0.409 >>>> 4.00000 4.00000 4.00000 >>>> >>>> *grompp.mdp:* >>>> >>>> >>>> title = Yo >>>> cpp = /usr/bin/cpp >>>> include = >>>> define = >>>> >>>> integrator = md >>>> tinit = 0 >>>> dt = 0.002 >>>> nsteps = 10000 >>>> init_step = 0 >>>> comm-mode = Linear >>>> nstcomm = 1 >>>> comm-grps = >>>> >>>> bd-temp = 300 >>>> bd-fric = 0 >>>> ld-seed = 1993 >>>> >>>> nstxout = 0 >>>> nstvout = 0 >>>> nstfout = 0 >>>> nstcheckpoint = 1000 >>>> nstlog = 50 >>>> nstenergy = 50 >>>> nstxtcout = 50 >>>> xtc-precision = 1000 >>>> xtc-grps = >>>> energygrps = >>>> >>>> nstlist = 3 >>>> ns_type = grid >>>> pbc = xyz >>>> rlist = 0.9 >>>> domain-decomposition = no >>>> >>>> coulombtype = Cut-off >>>> rcoulomb-switch = 0 >>>> rcoulomb = 0.9 >>>> epsilon-r = 1 >>>> vdw-type = Cut-off >>>> rvdw-switch = 0 >>>> rvdw = 1.2 >>>> DispCorr = EnerPres >>>> table-extension = 1 >>>> >>>> Tcoupl = berendsen >>>> tc-grps = System >>>> tau_t = 0.1 >>>> ref_t = 300 >>>> Pcoupl = berendsen >>>> Pcoupltype = isotropic >>>> tau_p = 0.1 >>>> compressibility = 4.5e-5 >>>> ref_p = 1.0 >>>> andersen_seed = 815131 >>>> >>>> gen_vel = yes >>>> gen_temp = 100 >>>> gen_seed = 1993 >>>> >>>> constraints = none >>>> morse = no >>>> >>>> energygrp_excl = >>>> >>>> >>>> You're not actually simulating in the gas phase with these parameters, >>> and >>> I'm surprised the simulation worked at all. With pressure coupling, the >>> unit cell should probably have collapsed, and even if it didn't, you're >>> simulating in some sort of pseudo-crystal state. I posted about this >>> yesterday... >>> >>> In any case, what you should be doing is more along the lines of: >>> >>> pbc = no >>> rvdw = 0 >>> rcoulomb = 0 >>> rlist = 0 >>> nstlist = 0 >>> pcoupl = no >>> >>> This will give you a fixed neighbor list with infinite cutoffs in a more >>> reasonable representation of the gas phase. >>> >>> -Justin >>> >>> *topol.top:* >>> >>>> >>>> >>>> #include "amber03.ff/forcefield.itp" >>>> #include "silver.itp" >>>> >>>> [ moleculetype ] >>>> 0001Clust 1 >>>> >>>> [ atoms ] >>>> 1 Ag 1 Ag Ag 1 0.000 >>>> >>>> [ system ] >>>> Bulk silver >>>> >>>> [ molecules ] >>>> 0001Clust 125 >>>> >>>> *silver.itp:* >>>> >>>> >>>> [ atomtypes ] >>>> Ag 107.8682 0.0 A 3.3156e-1 9.6468e-5 >>>> >>>> >>>> -- >>> ==============================****========== >>> >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> > >>> >>> ==============================****========== >>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to [email protected]. >>> * Can't post? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? 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