Re: simulating TIP4P with NAMD 2.7b2

From: Peter Freddolino (
Date: Tue Mar 16 2010 - 14:42:36 CDT

Hi Guillaume,
TIP4 is broken in NAMD 2.7b2 because of an error in the logic handling
lone pairs. Either 2.7b1 or (preferrably) the cvs version should work.

Guillaume Stirnemann wrote:
> Dear all,
> I am trying to simulate a box of pure TIP4P water with NAMD 2.7b2. As
> stated in the user's guide, I am using the keyword:
> waterModel tip4
> in the configuration file. In the pdb file, I respect the order
> suggested in the manual (oxygen, hydrogen, hydrogen, lone pair) and
> treat the lone pair as a regular atom in the psf file, as well as in
> the parameters file.
> However, the simulation crashes and I got the following message :
> FATAL ERROR: must have same number of LP hosts as lone pairs
> I guess this has something to do with the way I declare lone pairs in
> my files (ie as regular atoms), but I do not know if there is a
> different way to do it, especially in the psf file. I cannot find any
> support on the Web or in the existing documentation.
> Could you please help me? Does someone already simulate a box of TIP4P
> water with this program?
> Thanks!
> With best regards
> Guillaume Stirnemann
> PhD Student
> Ecole normale superieure, Paris (France)
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