Re: namd 2.9 tip4p-2005

From: Guanglei Cui (amber.mail.archive_at_gmail.com)
Date: Thu Apr 11 2013 - 10:31:33 CDT

I am having a similar issue when trying to use TIP4P with AMBER files
(namd2.9). The files were prepared with "set default flexiblewater on",
which is the reported solution previously. I see the same "ERROR" lines for
each water molecule in the system, presumably for the lone pairs (LP or
EPW, both names tried), with no further detail. The minimization would run
for some steps, but eventually bombs. The ERROR messages might be generated
in Molecule.C line 2429-2430. But I can't be sure.

    if ( (atoms[i].mass<1.5) != (lcpoParamType[i]==0) ) {
      CkPrintf("ERROR\n");

It sounds like people on the list have reported success in using TIP4P with
AMBER input files and NAMD. I appreciate if anyone can share the exact
steps to get this working.

Cheers,
Guanglei

On Wed, Jan 16, 2013 at 1:01 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> I would suggest finding the code lines printing this message. The water
> models are hardcoded in NAMD so it is possible that there are problems to
> get some parameters. Also, the order of the atoms per solvent is important.
> Did you pass the parameter watermodel tip4 (or similar)?****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Daniele Gentili
> *Gesendet:* Dienstag, 15. Januar 2013 13:23
> *An:* namd-l_at_ks.uiuc.edu
> *Betreff:* namd-l: namd 2.9 tip4p-2005****
>
> ** **
>
> Dear namd users.****
>
> I am running a simulation containing tip4p2005 water model built****
>
> with psfgen and with the correct topology file.****
>
> During the run it appears the line "ERROR" *for a number of time*****
>
> *equal to the number of water molecules*.****
>
> than the program continue it's run printing energies.****
>
> ** **
>
> what is going on ?****
>
> ** **
>
> thank you****
>
> ** **
>
> Daniele Gentili****
>

-- 
Guanglei Cui

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