simulating TIP4P with NAMD 2.7b2

From: Guillaume Stirnemann (
Date: Tue Mar 16 2010 - 08:33:48 CDT

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?


With best regards

Guillaume Stirnemann
PhD Student
Ecole normale superieure, Paris (France)

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