Luther,
I actually thought I would switch off an atom`s charge and LJ interactions if I transform it into a dummy atom. Is this wrong? I am worried about the mass of the atom a heavy hydrogen is attached to. In an amino group with heavy hydrogens the mass of the nitrogen is decreased to about 8u since some of its mass is transferred to the hydrogens. If I want to make a hydroxyl group of the amino group in thermodynamic integration one of the hydrogens has to become a dummy atom. My question is whether I should decrease the mass of the oxygen as it is connected to the heavy dummy atom. I wouldn't decrease its mass if the dummy atom were derived from a normal hydrogen but what shall I do in the case of a heavy hydrogen? I am pretty sure that the decision will have an effect on momentum space and therefore the outcome of the thermodynamic integration.
I've never done anything with heavy hydrogens, but I think if you are going to turn an amino group into a hydroxyl group, you want to end up with a hydroxyl group that has the right mass, so this is something that is right to be concerned about. I can't say anything too definitive, but my advice is to make sure you end up with the right end states, even if it involves changing masses. I think normally if you involve some transformation which involves changing one atom type into another with a different mass, you WILL have a d(Ekin)/dlambda term which makes a contribution to the free energy of the transformation. David
Best Luther > Message: 1 > Date: Tue, 16 May 2006 09:53:27 +0200 > From: Lars Schaefer <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] TI and heavy H > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Luther, > why do you want to switch the charges of your heavy H's off? You could > just switch the charges and LJ interactions off, and leave the masses > as they are. > Best, > Lars > > [EMAIL PROTECTED] wrote: > >>Dear Gromacs users, >> >>I want to perform a thermodynamic integration using heavy H´s in my >>system. I am somewhat confused about how to deal with dummy atoms that >>originate from heavy H´s. Do I still have to substract the appropriate >>mass from the atom the dummy atom is attached to? I suppose I would >> change >>the momentum part of phase space otherwise. >> >>Cheers >> >>Luther >> >>_______________________________________________ >>gmx-users mailing list gmx-users@gromacs.org >>http://www.gromacs.org/mailman/listinfo/gmx-users >>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 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
