[gmx-users] Re:gmx-users Digest, Vol 67, Issue 150 memory allocation

hema dhevi hema_gromacs at in.com
Tue Dec 1 08:41:36 CET 2009

 hai justin,ya i am working on actual KALP tutorial onlyhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmxtutorials/membraneprotein/index.htmland i am using the pdb file which is given in the website. This is the first time i am doing MD simulation for transmembrane proteins before using the protein of my interest i tried it with the peptide given the tutorial.hereby i am attaching the .mdp file which i am using ; minim.mdp  used as input into grompp to generate em.tpr; Parameters describing what to do, when to stop and what to saveintegrator= steep; Algorithm (steep = steepest descent minimization)emtol= 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nmemstep= 0.01; Energy step sizensteps= 50000; Maximum number of (minimization) steps to perform; Parameters describing how to find the neighbors of each atom and how to calculate the interactionsnstlist= 1; Frequency to update the neighbor list and long range forcesnstype= grid; Method to determine n
 eighbor list (simple, grid)rlist= 1.2; Cutoff for making neighbor list (short range forces)coulombtype= PME; Treatment of long range electrostatic interactionsrcoulomb= 1.2; Shortrange electrostatic cutoffrvdw= 1.2; Shortrange Van der Waals cutoffpbc= xyz ; Periodic Boundary Conditions (yes/no)thank youwith regards,N.Hema Dhevi
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