On Tuesday 09 June 2009 18:27:16 Berk Hess wrote: > > From: [email protected] > > To: [email protected] > > Subject: Re: [gmx-users] Shell dynamics with vdW terms. > > Date: Tue, 9 Jun 2009 16:29:39 +0200 > > > > On Tuesday 09 June 2009 10:02:47 Berk Hess wrote: > > > Hi, > > > > > > The equation you refer to is only an initial guess for the > > > optimization. The positions of the shells are optimized using the > > > forces from the full potential function. > > > > > > Berk > > > > > > > From: [email protected] > > > > To: [email protected] > > > > Date: Tue, 9 Jun 2009 09:51:13 +0200 > > > > Subject: [gmx-users] Shell dynamics with vdW terms. > > > > > > > > Hello, > > > > > > > > I have some troubles understanding the way used by Gromacs in > > > > optimizing the position of shells. In section 3.5.1 the manual says > > > > that the force on a shell particle is decomposed into two terms. The > > > > first represents the polarization and the second includes the Coulomb > > > > and van der Waals interactions. It continues assuming that the second > > > > term is constant and derives an analytic expression to calculate the > > > > shell position. > > > > > > > > My troubles arise after reading the paper: J. Phys. Chem. B 2009, > > > > 113, 7270-7281 by A. Villa, B. Hess & H. Saint-Martin. In the paper > > > > they simulate Lanthanides in water. In Table 2 they assign a 1/r**12 > > > > term to the ion-shell - water-shell interaction (the A_MIM > > > > parameter). I believe that this term is used in eq. 8 of the > > > > Supporting Information. Because is vdW like it seems to me that it > > > > breaks the previously mentioned assumption of vdW constancy. > > > > > > > > Could anybody help me? > > > > > > > > Thanks a lot. > > > > > > > > Rafael > > > > > > > > -- > > > > Dr. Rafael R. Pappalardo > > > > Dept. of Physical Chemistry, Univ. de Sevilla (Spain) > > > > e-mail: [email protected] > > > > _______________________________________________ > > > > gmx-users mailing list [email protected] > > > > http://lists.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 > > > > > > _________________________________________________________________ > > > See all the ways you can stay connected to friends and family > > > http://www.microsoft.com/windows/windowslive/default.aspx > > > > Dear Berk, > > > > thanks for the quick answer. > > > > I am having lot of troubles trying to minimize a cation+1 water molecule > > using Gromacs 4.0.5. The minimization proceeds without warnings but at a > > certain point it seems that the shell minimizer does not work ok. The > > kind of structures I am obtaining are: > > Generated by trjconv : Cf in Water t= 9.00000 > > 6 > > 1Cf_s Cf 1 1.49566 1.61167 1.73228 > > 1Cf_s Ms 2 1.49450 1.62107 1.72892 > > 2SOL OW 3 1.51913 1.41088 1.80113 > > 2SOL HW1 4 1.51596 1.36681 1.89843 > > 2SOL HW2 5 1.53786 1.31814 1.75093 > > 2SOL MW 6 1.51789 1.42144 1.79730 > > 3.10740 3.10740 3.10740 > > Generated by trjconv : Cf in Water t= 10.00000 > > 6 > > 1Cf_s Cf 1 1.49838 1.58947 1.74003 > > 1Cf_s Ms 2 1.49587 1.60861 1.73299 > > 2SOL OW 3 1.51772 1.42189 1.79765 > > 2SOL HW1 4 1.51568 1.37036 1.89631 > > 2SOL HW2 5 1.53733 1.32238 1.75035 > > 2SOL MW 6 1.51602 1.43730 1.79166 > > 3.10740 3.10740 3.10740 > > Generated by trjconv : Cf in Water t= 11.00000 > > 6 > > 1Cf_s Cf 1 1.50510 1.52690 1.75928 > > 1Cf_s Ms 2 1.50102 1.57015 1.74742 > > 2SOL OW 3 1.51647 1.43148 1.79236 > > 2SOL HW1 4 1.51461 1.38178 1.89116 > > 2SOL HW2 5 1.53582 1.33543 1.74711 > > 2SOL MW 6 1.50797 1.50425 1.77168 > > 3.10740 3.10740 3.10740 > > > > I see no warning or error in the md.log file albeit the Coulomb energy is > > rather large. The run continues at to t=50.000 with the message: > > > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 0.1 > > > > Could I sent you the input files in order to get some advice? > > > > > > Best regards, > > > > Rafael > > > > -- > > Dr. Rafael R. Pappalardo > > Dept. of Physical Chemistry, Univ. de Sevilla (Spain) > > e-mail: [email protected] > > At this point I have no clue if there might be something wrong at all. > There are many questions to ask: > What energies would you expect? > Have you checked if the minimized structure looks reasonable?
Yes, I have checked the structures. During the minimization the charges on the cation nucleus and the mobile charge on the oxygen collapse. > Is this a force field from the literature that it proven to work with this > water model? Polarizable models are tricky, if there is not enough > repulsion or the spring constant is too weak you can easily get a > polarization catastrophe. > > Berk > The force field is an in house development. We have tried the minimization using DL-POLY and a Monte Carlo code and the final result seems sensible. The troubles are with Gromacs. We have checked that the initial energy is the same between Gromacs and DL-POLY. Thanks again. > > _________________________________________________________________ > What can you do with the new Windows Live? Find out > http://www.microsoft.com/windows/windowslive/default.aspx -- Dr. Rafael R. Pappalardo Dept. of Physical Chemistry, Univ. de Sevilla (Spain) e-mail: [email protected] _______________________________________________ gmx-users mailing list [email protected] http://lists.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
