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Dear Users <br><br>I have a peptide, (1AKI.pdb)<br><br>My aim is to solvate it in the presence of the explicit water molecules<br>and do minimization and to split the energy terms , and to see the energy contribution from each terms <br><br>for this i have done the following in gromacs <br><br>-----------------------------------------------------------------------------------<br>pdb2gmx -ignh -ff gromos43a1 -f 1AKI.pdb -o 1AKI_processed.gro -water spc<br>editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic<br>genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top<br>grompp -f minim.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr<br>mdrun -v -deffnm em<br>------------------------------------------------------------------------------------<br><br>the minim.mdp file is as follows <br><br>---------------------------------------------------<br>define = -DFLEXIBLE<br>constraints = none<br>integrator = cg<br>dt = 0.001 ; ps !<br>nsteps = 1000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.0<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 10.0<br>emstep = 0.01<br><br>energygrps = protein SOL<br>------------------------------------------------<br><br>in the above i have given the energy groups, protein and solvent <br><br>after minimization one can get the energy values from all the possible contributions as follows<br><br>g_energy -f em.edr<br><br>in this term it is not possible to separate the bond distance and the bond angle term for the protein and water separately, <br><br>How to get these terms separately for water and the protein for this minimized structure ? ( for a single structure)<br><br>I can not under stand the earlier explanation , could any one can tell in detail <br><br>thanks in advance <br><br><br><br><br><br><br><br><br> </div></body>
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