<blockquote><gmx-users-request@gromacs.org><gmx-users@gromacs.org> </gmx-users@gromacs.org></gmx-users-request@gromacs.org>hai justin,<br><blockquote><br>ya i am working on actual KALP tutorial only<br><br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html<br><br>and i am using the pdb file which is given in the website. This is the first time i am doing MD simulation <br>for transmembrane proteins before using the protein of my interest i tried it with the peptide given the tutorial.<br><br>hereby i am attaching the .mdp file which i am using <br><br><pre>; minim.mdp - used as input into grompp to generate em.tpr<br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep Algorithm (steep = steepest descent minimization)<br>emtol = 1000.0 Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>emstep = 0.01 ; Energy step size<br>nsteps = 50000
Maximum number of (minimization) steps to perform<br><br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>nstlist = 1 Frequency to update the neighbor list and long range forces<br>ns_type = grid Method to determine neighbor list (simple, grid)<br>rlist = 1.2 Cut-off for making neighbor list (short range forces)<br>coulombtype = PME Treatment of long range electrostatic interactions<br>rcoulomb = 1.2 Short-range electrostatic cut-off<br>rvdw = 1.2 Short-range Van der Waals cut-off<br>pbc = xyz Periodic Boundary Conditions (yes/no)<br></pre><br>thank you<br><br>with regards,<br>N.Hema Dhevi<br><br><br><br><br></blockquote></blockquote>