Re: Using 4-site water model in NAMD

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Sep 16 2018 - 22:11:44 CDT

Dear Haohao,
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,
lone pair.**"

Your atom ordering does not obey this rule.

Best,
Peter

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_
> 8CAqX7LBsaenE4S.
>
> Could anyone help me out? Thanks!
>
> Best,
> Haohao
>

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