From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Sep 16 2018 - 22:11:44 CDT
At least one problem is quickly apparent. Quoting the namd manual on the
use of the TIP4 water model:
"Specifies the water model to be used. When using the TIP3P water model,
the ordering of atoms within each TIP3P water molecule must be oxygen,
hydrogen, hydrogen. **When using the TIP4P water model, the ordering of
atoms within each TIP4P water molecule must be oxygen, hydrogen, hydrogen,
Your atom ordering does not obey this rule.
On Sun, Sep 16, 2018 at 9:05 PM, Haohao Fu <fhh2626_at_gmail.com> wrote:
> Dear All,
> I'm trying to equilibrate a TIP4P water box using NAMD. However, when I
> submit such job, the NAMD process will stop in 10 timesteps. I suspect that
> there are something wrong in my psf file, but I cannot figure out where the
> problem is.
> I used the official version of "toppar_water_ions_tip4p.str" in
> http://mackerell.umaryland.edu/charmm_ff.shtml and tried both NAMD 2.12
> and 2.13b1. The "waterModel" option is set to "tip4". All the files used
> can be download in https://drive.google.com/open?id=1HCZLPU1uHnPplwMC_
> Could anyone help me out? Thanks!
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