<div>Dear Moeed:<br></div><div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>3. Use NVT (no barostat) if you really need some speficif density. Calculate the box size by hand.</div><div><br></div><div>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 ?</div>
<div><br></div><div>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.</div><div><br></div><div>6. Just equilibrate the system to avoid volume dances in the production run.</div>
<div><br></div><div>Good luck!</div><div><br>-- <br>Dr. Vitaly V. Chaban<br>Department of Chemistry<br>University of Rochester,<br>Rochester, NY, U.S.A.</div>
<div><br></div><div><br></div><div><br></div>
Dear Dr.Chaban,<br>
<br>
Thanks for your message. Now I have to groups: PE is a single chain and<br>
HEX (343 hexane molecules). I am interested in nonbonded interaction<br>
energies between PE and solvent as well as between PE-PE and HEX -HEX. I ran<br>
the simulation for 300ps and the system is equilibrating (300K and 30bar and<br>
also total energy relaxes to a 46000KJ/mol). Actually I can not trust these<br>
results since if you remember you got much less energy terms.. I was<br>
shameful of bothering you and discussing about that at that time since I<br>
thought it does not make sense getting different results with a same<br>
parameter file and gerometry. You said it might be because I am getting<br>
results in a different unit but in fact to get the energy break down I just<br>
issue g_energy command and dont touch anything. So energy values listed<br>
below should be in KJ/mol (MOLE by default and not molecule). Since H and C<br>
are the only atoms present in the system I have switched off electrostatics<br>
and total energy is about 46000KJ/mol. I would be thankful if you could take<br>
a look at my system in a proper time.<br>
<br>
I have also some other inquiries about this system:<br>
<br>
- the density I am getting is about 650 SI and I need sth about 400. In<br>
general the key parameter to change density in NPT is pressure right? so I<br>
could use P=20bar to get less density and it is kind of try and error . am I<br>
right?<br>
<br>
- I have still a foggy image of the system size in simulations. How can I<br>
decide on number of polymer and solvent particles in system? (of course the<br>
smaller the better in terms of simulation time..) but the reason I am asking<br>
this is because I ran simulations for different number of polymer chains<br>
(1,2,4,8) and I saw energy terms as total energy increase in value as<br>
systmes becomes larger. If units are in energy/mol so why is this happening?<br>
It does not make sense to calculate energy for a certain (MOLE) amount of<br>
molecules and get different values for different system size. (in brief: I<br>
can no t decide on number of polymer and hexane molecules)<br>
<br>
-now in this system there is only one polymer chain and energy breakdown<br>
shows energy for PE-PE LJ SR and 1-4. Does it make sanse to have SR within a<br>
single chain? (does this come from 1-5,1-6....interactions on chain? in case<br>
of hexane this can be only 1-5,1-6,1-7 becase there are no more than 7 bonds<br>
away each atom) LJ-SR:HEX-HEX = -7651.06, & LJ-SR:PE-PE =-96.7831<br>
<br>
-at the beginning of the simulation I see the system is decreasing in size<br>
and after about 10ps box expands again and after 20th ps starts contracting<br>
again. (volume starts from 8000 nm3 and reaches around 500 then increases to<br>
1600 nm3 and after that converges nicely to a plateau..). I tried both<br>
semiisotropic and isotropic options but the same behaviour has been<br>
observed.<br>
<br>
<br>
I appreciate any help and comment...<br>
Moeed :)<br>
<br>
**********************************************************************<br>
<br>
Energy Average RMSD Fluct. Drift<br>
Tot-Drift<br>
-------------------------------------------------------------------------------<br>
Bond 8536.6 562.056 441.004 4.02362<br>
1207.09<br>
Angle 13076.1 682.442 576.028 4.2256<br>
1267.69<br>
Ryckaert-Bell. 3276.27 329.245 302.614 -1.49785<br>
-449.355<br>
LJ-14 1762.95 58.3619 57.9592 0.0790304<br>
23.7092<br>
Coulomb-14 0 0 0<br>
0 0<br>
LJ (SR) -8457.99 2676.83 1915.36 -21.5925<br>
-6477.77<br>
Coulomb (SR) 0 0 0<br>
0 0<br>
Potential 18193.9 1946.39 1467.66 -14.7621<br>
-4428.64<br>
Kinetic En. 27009.8 325.523 325.51 0.0343522<br>
10.3057<br>
Total Energy 45203.7 1970 1501.36 -14.7277<br>
-4418.33<br>
Temperature 299.914 3.61457 3.61442 0.000381443<br>
0.114433<br>
Pressure (bar) 30.8942 533.069 533.059 0.0378739<br>
11.3622<br>
Box-X 5.41674 2.51691 2.19253 -0.0142718<br>
-4.28156<br>
Box-Y 5.41674 2.51691 2.19253 -0.0142718<br>
-4.28156<br>
Box-Z 5.02579 2.60455 2.00013 -0.0192635<br>
-5.77908<br>
Volume 306.955 929.783 856.612 -4.17472<br>
-1252.42<br>
Density (SI) 530.808 191.837 139.2 1.52423<br>
457.271<br>
#Surf*SurfTen -3.00385 3396.99 3396.96 0.165929<br>
49.779<br>
Coul-SR:PE-PE 0 0 0<br>
0 0<br>
LJ-SR:PE-PE -96.7831 12.0843 11.971 0.0190581<br>
5.71744<br>
Coul-14:PE-PE 0 0 0<br>
0 0<br>
LJ-14:PE-PE 145.957 10.2536 10.2529 0.00134961<br>
0.404885<br>
Coul-SR:PE-HEX 0 0 0<br>
0 0<br>
LJ-SR:PE-HEX -710.145 226.458 156.934 -1.88519<br>
-565.559<br>
Coul-14:PE-HEX 0 0 0<br>
0 0<br>
LJ-14:PE-HEX 0 0 0<br>
0 0<br>
Coul-SR:HEX-HEX 0 0 0<br>
0 0<br>
LJ-SR:HEX-HEX -7651.06 2451.43 1758.13 -19.7263<br>
-5917.92<br>
Coul-14:HEX-HEX 0 0 0<br>
0 0<br>
LJ-14:HEX-HEX 1616.99 56.0996 55.6947 0.0776808<br>
23.3043<br>
<br>
*************************************************************************<br>
pbc = xyz ; use priodic BCs in all<br>
directions<br>
energygrps = PE HEX<br>
<br>
; Run control<br>
integrator = md<br>
dt = 0.001<br>
nsteps = 300000<br>
nstcomm = 1<br>
<br>
; Output control<br>
nstenergy = 100<br>
nstxout = 100<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000<br>
nstxtcout = 0<br>
<br>
; Neighbor searching<br>
nstlist = 10 ;<br>
ns_type = grid<br>
<br>
; Electrostatics/VdW<br>
;coulombtype = PME<br>
vdw-type = Shift<br>
rcoulomb-switch = 0<br>
rvdw-switch = 0.9<br>
<br>
; Cut-offs<br>
rlist = 1.1<br>
rcoulomb = 1.1 ;1.0<br>
rvdw = 1.0<br>
<br>
; Temperature coupling<br>
Tcoupl = v-rescale<br>
tc-grps = System<br>
tau_t = 0.1<br>
ref_t = 300<br>
<br>
; Pressure coupling<br>
Pcoupl = Parrinello-Rahman;berendsen<br>
Pcoupltype = semiisotropic ;isotropic ;<br>
tau_p = 1 1<br>
compressibility = 4.5e-5 4.5e-5<br>
ref_p = 30.0 30.0<br>
<br>
; Velocity generation<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
; Bonds<br>
constraints = none<br>
constraint-algorithm = lincs<br> <font color="#888888">
</font><br><br>