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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