Hi everybody , I run simulation of 4 same molecule keep apart in box of 4 4 4 dimension ..( 71 atom in one molecule = 71 * 4 = total atom are 284 ) force field = gromacs96 53a6
COM (center of mass) infirmation of molecules system size : 1.255 1.577 1.883 box vectors : 4.000 4.000 4.000 (nm) mol1 : 2.057 0.844 1.941 mol 2 : 2.057 0.844 3.141 mol 3 : 2.057 3.244 0.744 mol 4 : 2.057 3.244 3.141 (Four molecule are kept at the four corner of square of each side 2.4 nm four molecule are catenated in same pdb ) my md.mdp input is like the .. ;Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT With command g_mindist , select option - 1 (Protein ) I got the following result.. The shortest periodic distance is 0.141718 (nm) at time 7692 (ps), between atoms 26 and 111 Is the simulation is behaving abnormal(I.e simulation is wrong ) or I have to select the option system on prompting ??? I am very new to these simulation field.. so all suggestion are appreciable ...
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