>Message: 3 >Date: Thu, 16 Dec 2010 11:50:51 -0500 >From: Vitaly Chaban <[email protected]> >Subject: [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not > high >To: [email protected] >Cc: gromacs <[email protected]> >Message-ID: > <[email protected]> >Content-Type: text/plain; charset=ISO-8859-1 > >> From: gromacs <[email protected]> >> Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not high > >> Hi, >> >> I want to simulate 3x3x0.8 water film (bulk water) first creat the water, >> >> genbox -cs -o film.gro -box 3 3 0.8 >> >> then, i EM the bulk water; >> >> Using steep, but >> >> t = 0.011 ps: Water molecule starting at atom 298 can not be settled. >> Check for bad contacts and/or reduce the timestep. >> Wrote pdb files with previous and current coordinates >> >> >> then i run, and i get the result. I use NPT, and T=300K. I run several >> times, but the final T was still 411K. >> >> >> >> So what could i do to get EM process successful? >> >> And what is the reason ? why i can not control the T 300K? >> >> >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> ------------------------------------------------------------------------------- >> Potential -9496.38 136.145 135.455 -0.158085 >> -47.4256 >> Kinetic En. 2358.2 73.5876 73.5471 -0.0281891 >> -8.45676 >> Total Energy -7138.19 136.284 135.326 -0.186274 >> -55.8824 >> Temperature 411.945 12.8548 12.8477 -0.00492426 >> -1.47728 >> Pressure (bar) -1.66406 704.355 704.355 -0.00424907 >> -1.27473 >> Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 >> -0.00233479 >> Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 >> -0.00233479 >> Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 >> -0.000622609 >> Density (SI) 1038.7 13.6165 13.5998 0.00778513 >> 2.33555 >> Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) > > > >Hey, gromacs - > >Nice to hear from you here... It is a bad idea to simulate something >with any cartesian dimension lower than a couple of nanometers using >classical FFs. All your problems are generated by 0.8 nm of the >z-side. > >-- >Dr. Vitaly V. Chaban >Rochester, U.S.A. > > >------------------------------ > Thanks very much. I use the cutoff=0.38, because the cutoff should be smaller than the half box size. I guess it may be the Z dimension is too small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all results are OK. My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9 to form interface. So if i want to run run bulk 3x3x0.8 water, how could i do? which FF should i use? the high T may be due to EM not success??
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