Sorry, I wasn't too clear in the first message. I will be using OpenMM Gromacs, which does support implicit solvent. My current energy minimization steps only lower the energy to -5E3. Is this okay considering water is not around? Is is necessary to do equilibration if I am using implicit solvent? Is so, can anyone direct me to reasonable parameters?
Thanks! Grace On Wed, Apr 15, 2009 at 2:55 AM, Mark Abraham <[email protected]>wrote: > Grace Tang wrote: > >> Hello All, >> >> I am doing energy minimization on a protein crystal structure to relax it. >> Afterwards, I plan to run md simulation with implicit solvent. I am new at >> this and have many questions. >> 1. Should the implicit solvent conditions be enabled when I run the energy >> minimization? >> > > No - while GROMACS has some vestiges in the user interface of an earlier > attempt to implement implicit solvation simulations, these will not > functional until at least version 4.1. > > 2. What minimum potential energy should I expect (i know that when >> explicit water is present, the energy often reaches -10E5 or -10E6) >> > > Negative, and vaguely proportional to the number of atoms. > > 3. What kind of emtol is appropriate? Is it better to set it high so that >> the system converges, or is it okay if machine precision is reached. >> > > It's pretty much irrelevant for preparing a system for MD. You'll have to > equilibrate it later, and the value of an EM step is merely relieving any > bad atom-atom contacts before they turn into huge accelerations. If the > equilibration doesn't crash, you did enough EM. > > Mark > > Below are 2 example runs I did with implicit_solvent = no >> When I decreased the step size, the system did not converge anymore. I >> was wondering if this was due to chance, precision issues (I am using single >> precision), or perhaps the emstep = 0.1 was reaching a nearby minimum and >> 0.01 was reaching the local minimum. Note, maximum force gets rather large >> when convergence is to machine precision. >> >> emtol = 1000 >> emstep = 0.1 >> Steepest Descents converged to Fmax < 1000 in 29 steps >> Potential Energy = -4.9613008e+003 >> Maximum force = 6.4596338e+002 on atom 235 >> Norm of force = 1.0625026e+002 >> >> emtol = 1000 >> emstep = 0.01 >> Steepest Descents converged to machine precision in 25 steps, >> but did not reach the requested Fmax < 1000. >> Potential Energy = -3.9642480e+003 >> Maximum force = 5.1200122e+003 on atom 416 >> Norm of force = 3.6602789e+002 >> >> Any advice is greatly appreciated. Much thanks! >> - Grace >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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