Moeed wrote:
Hello Dr. Chaban,
System size is 5 *5*3 nm when density reaches around 600 SI. Can you
please explain what do you mean by "What about dependence heat of
evaporation vs system size ?". I dont know how to compute vap. heat in
gromacs!
Unfortunately, I am still unclear about energy units. :(
Yes, only when I use
g_energy -f ener.edr -o energy.xvg -nmol 8 I get pretty similar
values as you obtained (around 2200 KJ/molecule !? ) but then units
should be energy per molecule. I am confused because Before you had said
units are per mole. Without using -nmol 8 option total energy is around
20,000 (apparently g_energy by default gives KJ/mole)
Another reason I am confused is because
g_energy -f ener.edr -o energy.xvg according to manual chapter 2 should
give energies in KJ/mol and not system. I did some simulations for
different number of polymer chains in a big box. (1, 2, 4, 8 chains).
The magnitude of energy values increase as number of chains increase..My
question is if values are in the units of KJ/mol why let's say nonbonded
interaction energy values are increasing in value as number of molecuels
goes up? Should not the values be the same if we are referring to MOLE
number of molecules?
I know manual can not be wrong but from what I see it makes more sense
if unit is energy/system!
When dividing the energy of a system by the number of molecules (in a
homogeneous system), you are extracting what I believe is commonly referred to
as "configurational energy" which, for relatively simple systems, should
converge fairly quickly. The reason your total energy values increase with
system size is a simple matter of potential energy. More interactions mean that
the magnitude of the potential will increase, and likewise with the kinetic
energy, more particles that have velocity imply a greater sum.
You can convince yourself of this fact by running relatively short simulations
of water boxes, using, i.e. spc216.gro and then a larger construct from it.
Within a few hundred ps, you should get reasonably converged configurational
energies, though of course the total energy will be larger simply by virtue of
the system size.
Energies are in kJ/mol, no question. The extrapolation would be that a mole of
a given species in the given configuration would have this energy in kJ. For a
single molecule, the energy is whatever value you obtain divided by Avogadro's
number, which is a relatively unimportant quantity if you are interested in bulk
dynamics.
And for the record, I do *not* enjoy novel-length posts, rather complete ones
with sufficient detail to diagnose the issue :)
-Justin
Thanks,
2010/8/27 Vitaly Chaban <[email protected] <mailto:[email protected]>>
Dear Moeed:
1. Please note, this is Justin here who likes long descriptions but
I like those which are as short as possible. :-) Please formulate
your questions more specifically because I am too lazy (and busy
unfortunately) to read all your MD novels at ones.
2. If I said that the energy was given per mole, than it is given
per mole of molecules, not systems, be sure. Use g_energy -nmol XXX
where it is reasonable. I think your energy vlue before was correct,
just divide it by NMOL.
3. Use NVT (no barostat) if you really need some speficif density.
Calculate the box size by hand.
4. Polymers are rather specific MD systems. I think your 1 PE + 343
hexanes should be a minimal good composition. By the way, what is
the size of MD box in nmxnmxnm? What about dependence heat of
evaporation vs system size ?
5. If I am not mistaken "LJ-SR" is a total Lennard-Jones energy of
system except 1-4 interactions. If I am not true, please somebody
correct me.
6. Just equilibrate the system to avoid volume dances in the
production run.
Good luck!
--
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester,
Rochester, NY, U.S.A.
Dear Dr.Chaban,
Thanks for your message. Now I have to groups: PE is a single
chain and
HEX (343 hexane molecules). I am interested in nonbonded interaction
energies between PE and solvent as well as between PE-PE and HEX
-HEX. I ran
the simulation for 300ps and the system is equilibrating (300K and
30bar and
also total energy relaxes to a 46000KJ/mol). Actually I can not
trust these
results since if you remember you got much less energy terms.. I was
shameful of bothering you and discussing about that at that time since I
thought it does not make sense getting different results with a same
parameter file and gerometry. You said it might be because I am getting
results in a different unit but in fact to get the energy break down
I just
issue g_energy command and dont touch anything. So energy values listed
below should be in KJ/mol (MOLE by default and not molecule). Since
H and C
are the only atoms present in the system I have switched off
electrostatics
and total energy is about 46000KJ/mol. I would be thankful if you
could take
a look at my system in a proper time.
I have also some other inquiries about this system:
- the density I am getting is about 650 SI and I need sth about 400. In
general the key parameter to change density in NPT is pressure
right? so I
could use P=20bar to get less density and it is kind of try and
error . am I
right?
- I have still a foggy image of the system size in simulations. How
can I
decide on number of polymer and solvent particles in system? (of
course the
smaller the better in terms of simulation time..) but the reason I
am asking
this is because I ran simulations for different number of polymer chains
(1,2,4,8) and I saw energy terms as total energy increase in value as
systmes becomes larger. If units are in energy/mol so why is this
happening?
It does not make sense to calculate energy for a certain (MOLE)
amount of
molecules and get different values for different system size. (in
brief: I
can no t decide on number of polymer and hexane molecules)
-now in this system there is only one polymer chain and energy breakdown
shows energy for PE-PE LJ SR and 1-4. Does it make sanse to have SR
within a
single chain? (does this come from 1-5,1-6....interactions on chain?
in case
of hexane this can be only 1-5,1-6,1-7 becase there are no more than
7 bonds
away each atom) LJ-SR:HEX-HEX = -7651.06, & LJ-SR:PE-PE =-96.7831
-at the beginning of the simulation I see the system is decreasing
in size
and after about 10ps box expands again and after 20th ps starts
contracting
again. (volume starts from 8000 nm3 and reaches around 500 then
increases to
1600 nm3 and after that converges nicely to a plateau..). I tried both
semiisotropic and isotropic options but the same behaviour has been
observed.
I appreciate any help and comment...
Moeed :)
**********************************************************************
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Bond 8536.6 562.056 441.004 4.02362
1207.09
Angle 13076.1 682.442 576.028 4.2256
1267.69
Ryckaert-Bell. 3276.27 329.245 302.614 -1.49785
-449.355
LJ-14 1762.95 58.3619 57.9592 0.0790304
23.7092
Coulomb-14 0 0 0
0 0
LJ (SR) -8457.99 2676.83 1915.36 -21.5925
-6477.77
Coulomb (SR) 0 0 0
0 0
Potential 18193.9 1946.39 1467.66 -14.7621
-4428.64
Kinetic En. 27009.8 325.523 325.51 0.0343522
10.3057
Total Energy 45203.7 1970 1501.36 -14.7277
-4418.33
Temperature 299.914 3.61457 3.61442 0.000381443
0.114433
Pressure (bar) 30.8942 533.069 533.059 0.0378739
11.3622
Box-X 5.41674 2.51691 2.19253 -0.0142718
-4.28156
Box-Y 5.41674 2.51691 2.19253 -0.0142718
-4.28156
Box-Z 5.02579 2.60455 2.00013 -0.0192635
-5.77908
Volume 306.955 929.783 856.612 -4.17472
-1252.42
Density (SI) 530.808 191.837 139.2 1.52423
457.271
#Surf*SurfTen -3.00385 3396.99 3396.96 0.165929
49.779
Coul-SR:PE-PE 0 0 0
0 0
LJ-SR:PE-PE -96.7831 12.0843 11.971 0.0190581
5.71744
Coul-14:PE-PE 0 0 0
0 0
LJ-14:PE-PE 145.957 10.2536 10.2529 0.00134961
0.404885
Coul-SR:PE-HEX 0 0 0
0 0
LJ-SR:PE-HEX -710.145 226.458 156.934 -1.88519
-565.559
Coul-14:PE-HEX 0 0 0
0 0
LJ-14:PE-HEX 0 0 0
0 0
Coul-SR:HEX-HEX 0 0 0
0 0
LJ-SR:HEX-HEX -7651.06 2451.43 1758.13 -19.7263
-5917.92
Coul-14:HEX-HEX 0 0 0
0 0
LJ-14:HEX-HEX 1616.99 56.0996 55.6947 0.0776808
23.3043
*************************************************************************
pbc = xyz ; use priodic BCs in all
directions
energygrps = PE HEX
; Run control
integrator = md
dt = 0.001
nsteps = 300000
nstcomm = 1
; Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 0
; Neighbor searching
nstlist = 10 ;
ns_type = grid
; Electrostatics/VdW
;coulombtype = PME
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0.9
; Cut-offs
rlist = 1.1
rcoulomb = 1.1 ;1.0
rvdw = 1.0
; Temperature coupling
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = Parrinello-Rahman;berendsen
Pcoupltype = semiisotropic ;isotropic ;
tau_p = 1 1
compressibility = 4.5e-5 4.5e-5
ref_p = 30.0 30.0
; Velocity generation
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = none
constraint-algorithm = lincs
--
Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php
Web:http://mmrg.chemeng.mcgill.ca/
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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