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