[gmx-users] Re: NPT simulation
Vitaly Chaban
vvchaban at gmail.com
Fri Aug 27 18:30:55 CEST 2010
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
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