From: Alessio Alexiadis (sersunzo_at_yahoo.com)
Date: Mon Jul 09 2007 - 09:52:47 CDT
In the last days I asked some questions about the use of TIP4P model in NAMD. I got some answers but basically everybody began his/her email with “I never used TIP4P model but I think…”. So I’m wondering if there is anybody who actually used this model.
The basic point is that the dummy atom (the forth site 'M' of the TIP4P) has mass 0.00 and it gives problems with the Rattle algorithm (or other constrain algorithms).
I can add a small mass (i.e. 0.01 amu) to this site but, I must also reduce the time step to 0.1 fs which is really too small.
Furthermore, all this is silly because it is not necessary to calculate the position of a dummy atom, which sould be automatically placed at the right position once the molecule moved.
Thus, please, if anybody has actually used this model with NAMD can provide a piece of advice?
PS. I attached to this email a small .pdb, .psf, .inp and .conf files for a very simple simulations with only two TIP4P water molecules. If you run it you will see what I mean.
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