Hello Justin,
[Actually, the reason I posted some parts of my mdp file was because you said I am sending redundant information so I just deleted the first lines of mdp file :) ] To get the xtc file initially I used nrexcl=3 in the top file. Then I used mdrun -rerun to breakdown energies on this xtc file with new top file nrexcl=7 to exclude all intramolecular nonbonded interactions (you definitely recall all these details :) 1- Does it matter in the first run (to get xtc) what option I use for nrexcl in top file. Actually, I thought maybe in the normal run I have to set this option to zero. I did that and I got lincs warning (the same applies for nrexcl=1). So I tried nrexcl=2 and I noticed the results are not the same as nrexcl 3. However, this means I am still having nonbonded intramolecular interaction between atoms that are less than 2 bonds away. Am I right? 2- I am wondering why in this breakdown I still see LJ and coloumb 1-4 interactions while I have nrexcl=2. 3- In the second set of results (nrexcl=3) potential energy is 2766 > 2156 (the value for nrexcl==2). Logically, when 3 bonds away are excluded potential energy should be less I think!.. 4- Regarding the units, in chapter 2 of manual the units for energy is in KJ/mol. Here is this table I see heat capacity is given in J/mol K. Could you please kindly tell me the units what is the unit for energy temrs LJ or coulomb? 5- Very important question: If I want to compute the interaction energies BETWEEN molecuels, do I have to sum up LJ (SR) =(-3026 e.g) and coloumb (SR)=74 ? and can I conclude that there is a net attraction energy in the system? 6- If I want to assure that equilibrium is reached, can I make the simulation time long enough such that T reaches 300 K? now it is 297 K. I appreciate your help. Thanks Moeed *mdrun -rerun on trajectory for nrexcl=2 in top file* Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Angle 4286.19 258.765 231.378 40.1269 401.349 Ryckaert-Bell. 722.966 69.0616 61.1677 11.1046 111.068 *LJ-14 498.432 31.2891 30.9138 1.67344 16.7378* * * *Coulomb-14 -322.264 11.5056 10.1507 1.87612 18.765* * * *LJ (SR) -3026.03 45.5198 38.6106 8.35011 83.5178* * * *Coulomb (SR) 74.4564 2.53605 2.53537 0.02034 0.203441* Coul. recip. -77.5276 2.3709 1.31777 -0.682623 -6.8276 Potential 2156.22 335.429 282.807 62.4689 624.814 Kinetic En. 0 0 0 0 0 Total Energy 2156.22 335.429 282.807 62.4689 624.814 Temperature 0 0 0 0 0 Pressure (bar) 1563.28 161.924 161.475 4.17097 41.718 Cons. rmsd () 0 0 0 0 0 Mu-X -0.00385475 0.893851 0.893682 -0.00602335 -0.0602456 Heat Capacity Cv: nan J/mol K (factor = nan) * * *mdrun -rerun on trajectory for nrexcl=3 in top file* Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 14 data sets All averages are over 501 frames Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Angle 4400.09 284.259 237.268 54.2184 542.293 Ryckaert-Bell. 1009.62 124.468 94.0379 28.2417 282.474 *LJ-14 648.411 40.6844 39.926 2.70793 27.0848* ** *Coulomb-14 -278.654 34.4227 11.8071 11.1987 112.01* ** *LJ (SR) -3010.16 47.968 42.5388 7.67736 76.789* ** *Coulomb (SR) 74.7846 2.5186 2.47007 0.170417 1.70451* Coul. recip. -78.0436 2.58606 1.54725 -0.717662 -7.17805 Potential 2766.05 454.268 342.141 103.497 1035.18 Kinetic En. 0 0 0 0 0 Total Energy 2766.05 454.268 342.141 103.497 1035.18 Temperature 0 0 0 0 0 Pressure (bar) 1973.01 177.068 172.803 13.3792 133.819 Cons. rmsd () 0 0 0 0 0 Mu-X -0.0523974 0.826473 0.826318 -0.00553723 -0.0553834 Heat Capacity Cv: nan J/mol K (factor = nan) ; Run control integrator = md dt = 0.002 ; ps ! nsteps = 5000 ; total 1.0 ps. nstcomm = 1 ; frequency for center of mass motion removal ; Output control nstenergy = 10 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps nstxout = 10 ; frequency to write coordinates/velocity/force to output trajectory file nstvout = 0 nstfout = 10 nstlog = 10 ; frequency to write energies to log file nstxtcout = 10 ; Neighbor searching nstlist = 10 ; neighborlist will be updated at least every 10 steps ;ns_type = grid ; Electrostatics/VdW coulombtype = PME vdw-type = cut-off ; Cut-offs rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Temperature coupling Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = HEX ;sol tau_t = 0.1 ;0.1 ref_t = 300 ;300 ; Pressure coupling: Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Velocity generation Generate velocites is on at 300 K. Manual p155 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ; Bonds constraints = all-bonds constraint-algorithm = lincs pbc=xyz
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