Hello Justin, I am trying to generate the top file for polyethylene chain using the information from the archive: http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html. In the former post you said parameters in the I am referring to are not necessarily correct.
1- By parameters you mean the coordinates in pdb file? The residues in this link seem correct to me but I am not sure if the hdb file is correct. 2- Could you please tell me how to generate a longer chain with the given residue types proposed in the above post. ATOM 1 C1 EthB 1 1.000 1.540 0.000 ATOM 2 C2 EthB 1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 EthE 3 3.912 5.623 0.000 ATOM 6 C2 EthE 3 5.368 6.124 0.000 END Here I do not see hydrogen atoms. I have created a long chain with 100 monomer units using Ascalaph designer. However the file is not properly formatted. i.e atoms are not numbered and residue name is missing. I do not want to alter the file by hand. Can you guide me how I can build a long chain with the residues you proposed in the above post (including hydrogen atoms) HETATM 1 C 1 2.739 2.554 -0.012 -0.390 C HETATM 2 H 1 2.736 3.644 -0.012 0.130 H HETATM 3 H 1 2.190 2.217 -0.893 0.130 H HETATM 4 H 1 2.190 2.217 0.868 0.130 H HETATM 5 C 2 4.155 1.993 -0.012 -0.260 C . . HETATM 291 H 97 72.086 -97.891 -0.012 0.130 H HETATM 292 H 97 70.558 -97.880 0.869 0.130 H HETATM 293 H 97 70.558 -97.880 -0.893 0.130 H 3- I have also an inquiry about the density of my solvent. One of the experts told me: Best thing you can do is, make a NPT simulation (look for the right compresibility) and look how much your density is off,if it's only a little your fine. I dont realize the statement "look how much your density is off"? The desnity is approx. 71000 Kg/m3 (4molecuels per nm3). From NPT run I see the density is 577 Kg/m3. and the volume is 30 nm3 (values from g_energy). How can I make sure if density changes are reasonable? *Volume * 30.9568* 0.374111 0.204815 Density (SI) *577.914* 6.97804 3.80252 Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Temperature 297.366 12.086 11.4021 1.38812 13.884 Pressure (bar) -30.0299 746.524 745.665 -12.3992 -124.017 *Volume 30.9568 0.374111 0.204815 -0.108427 -1.08449* ** *Density (SI) 577.914 6.97804 3.80252 2.02643 20.2684* pV -55.9879 1393.39 1391.81 -22.9985 -230.031 #Surf*SurfTen 218.21 4871.45 4871.37 -9.30662 -93.0848 T-HEX 297.366 12.086 11.4021 1.38812 13.884 Lamb-HEX 1.00011 0.000588089 0.000561362 -6.07045e-05 -0.000607166 Heat Capacity Cv: 12.5027 J/mol K (factor = 0.0016519) Isothermal Compressibility: 0.00011012 /bar Adiabatic bulk modulus: 9080.99 bar with mdp file: > ; Pressure coupling: Pressure coupling is not on > Pcoupl = berendsen > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 Thanks,
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