OK what seemed wrong to you?<br><br><div class="gmail_quote">On Mon, Jan 17, 2011 at 12:24 AM, bharat gupta <span dir="ltr"><<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>I am doin the first minimization step.. here are the details of minim.mdp file</div>
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<div>; 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</div>
<div>; 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 = 1.0 ; Cut-off for making neighbor list (short range forces)<br>coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.0 ; Short-range electrostatic cut-off<br>rvdw = 1.0 ; Short-range Van der Waals cut-off<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)</div><div><div></div><div class="h5">
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<div><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343</div>
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