Hello Justin Sir, Greetings from Pawan Thanks for your valuable suggestion and reply. Initially I gave the emtol of 1000 and the output I got was : Steepest Descents converged to machine precision in 163 steps but did not reach the requested Fmax<1000. Potential Energy = - 4.4516497e+05
Even I tried to minimize the popc bilayer which I took from Tieleman sir's website ( before generating a bigger bilayer using genconf ) but that also converged to machine precision but not to the requested Fmax<1000. How do I proceed further ? Thanks for your suggestions and help. Thanking you, Pawan On Thu, Mar 19, 2009 at 9:13 PM, > Pawan Kumar wrote: > > Hello Justin Sir, > > > > Greetings from Pawan > > Thanks for your valuable suggestion and reply. > > After inserting the protein in the bilayer using genbox I have minimized > > the whole system without using any position restraints (i.e. define = > > -DFLEXIBLE in em.mdp file). I used vanderwaal's distance parameter ( > > -vdwd of 0.6 ) in the genbox step. > > After running mdrun for energy minimization I got the output as : > > Steepest Descents converged to Fmax<2250 in 14 steps. > > Potential energy = - 6.9484700e+05 > > Maximum force = 2.2114819e+03 on atom 34277 > > Norm. of force = 5.0103039e+04 > > > > You should try for an Fmax of no greater than 1000. 2250 is still very > high. > > > I tried decreasing the emtol value in the em.mdp file but it ended with > > machine precision. > > How far did it converge? What was Fmax? > > > I have read in literature that 5000 steps of Steetest Descents run is > > required after inserting the protein in the bilayer which should be > > followed by atleast 1000 steps of conjugate gradients. How can I > > accomplish this ? Is there any parameter to be given in the em.mdp file > > ? I use steep as the integrator in the mdp file for energy minimization. > > Read the manual. > > Whether or not that exact setup is going to be "required" is likely > system-specific. I would say that as long as your system converges to a > stable, > negative Epot with a reasonable Fmax (less than 1000, but ideally lower) > then > you *may* have an appropriate starting structure. > > -Justin > > > Please help with some suggestions. > > Thanks in advance. > > > > Thanking you, > > Pawan > > > > > > >
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