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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: Wed, 10 Jun 2009 08:42:26 +0200<br>> <br>> On Tuesday 09 June 2009 18:27:16 Berk Hess wrote:<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<br>> > > > optimization. The positions of the shells are optimized using the<br>> > > > forces from 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<br>> > > > > optimizing the position of shells. In section 3.5.1 the manual says<br>> > > > > that the force on a shell particle is decomposed into two terms. The<br>> > > > > first represents the polarization and the second includes the Coulomb<br>> > > > > and van der Waals interactions. It continues assuming that the second<br>> > > > > term is constant and derives an analytic expression to calculate the<br>> > > > > shell position.<br>> > > > ><br>> > > > > My troubles arise after reading the paper: J. Phys. Chem. B 2009,<br>> > > > > 113, 7270-7281 by A. Villa, B. Hess & H. Saint-Martin. In the paper<br>> > > > > they simulate Lanthanides in water. In Table 2 they assign a 1/r**12<br>> > > > > term to the ion-shell - water-shell interaction (the A_MIM<br>> > > > > parameter). I believe that this term is used in eq. 8 of the<br>> > > > > Supporting Information. Because is vdW like it seems to me that it<br>> > > > > breaks the previously mentioned 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<br>> > > > > the 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>> > ><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<br>> > > using Gromacs 4.0.5. The minimization proceeds without warnings but at a<br>> > > certain point it seems that the shell minimizer does not work ok. The<br>> > > kind of 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>> <br>> Yes, I have checked the structures. During the minimization the charges on the <br>> cation nucleus and the mobile charge on the oxygen collapse.<br>> <br>> > Is this a force field from the literature that it proven to work with this<br>> > water model? Polarizable models are tricky, if there is not enough<br>> > repulsion or the spring constant is too weak you can easily get a<br>> > polarization catastrophe.<br>> ><br>> > Berk<br>> ><br>> <br>> The force field is an in house development. We have tried the minimization <br>> using DL-POLY and a Monte Carlo code and the final result seems sensible. The <br>> troubles are with Gromacs. We have checked that the initial energy is the same <br>> between Gromacs and DL-POLY.<br>> <br>> Thanks again.<br><br>But this is really pure energy minimization and not shell minimization during MD,<br>or did I misunderstand this?<br>During pure energy minimization (integrator steep or cg) the shells are treated<br>as any other particle, so there should be no particular shell issues at all.<br>But you could still have a polarization catastrophe. It could be that the initial<br>EM step (mdp parameter em_step) is too large.<br><br>Berk<br><br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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