On 1/11/13 6:33 AM, Alexej Mazheika wrote:
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.
AMBER force fields do not specify nonbonded parameters in terms of C6 and C12,
they are written as sigma and epsilon. If you're using C6 and C12 directly,
then the parameters are in fact wrong within the context of what the force field
expects. See the manual for the conversion equations or use g_sigeps.
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.
I wasn't sure what your source was for the parameters. I would still encourage
you to consult AMBER literature for how parameters are generally developed,
which typically includes QM calculations. Dealing with transition metals is a
tricky proposition for any of the force fields used in Gromacs. There's
definitely literature out there from people who have simulated metal particles,
so I would suggest you also investigate what those authors do and what
parameters they use.
-Justin
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>
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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>
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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
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