Re: [gmx-users] TI and heavy H

2006-05-16 Thread David Mobley
rmation. 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 > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain;

Re: [gmx-users] TI and heavy H

2006-05-16 Thread Mark Abraham
[EMAIL PROTECTED] wrote: Hi Lars, 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 nitroge

[gmx-users] TI and heavy H

2006-05-16 Thread reich
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 > Message-ID: <[EMAIL PROTECTED]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >

Re: [gmx-users] TI and heavy H

2006-05-16 Thread Lars Schaefer
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

[gmx-users] TI and heavy H

2006-05-15 Thread reich
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