From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Dec 20 2011 - 00:33:08 CST
Thanks for your interest.
Yes I followed the instructions from the tutorial. I think there's a version problem of the fcrmod or something, because we use the ambertools from amber 9/10. Here's what I did for a test:
2. loadamberparams frcmod.tip4p
3. set default flexiblewater on
4. WAT = TP4
5. a=loadpdb <- only a WAT box
6. saveamberparm a test.top test.crd <- lot of warning on short bonds of EPW and about duplicate angle
7. build namd script with watermodel tip4
8. mimimize & run
The simulation then seems to run as expected, but it doesn't. If one look the trajectory one see long chains of EPW->H with 1A distance and funny conformations of 3 waters that lay in each other.
I had very much trouble getting a TIP4P simulation to work. When I startet, I got problems with namd throwing segfaults. I solved that with taking the frcmod.tip4p file from the solvents folder. The default is another location what didn't work for me. The missing Angle for H-O-H is solved by setting flexiblewater. SO it seems the input should work but it doesn't.
Maybe namd is compatible only with a specific type of tip4p. I read something about tip4p 2005.
What do you think.
> -----Ursprüngliche Nachricht-----
> Von: George M Giambasu [mailto:giambasu_at_gmail.com]
> Gesendet: Montag, 19. Dezember 2011 17:17
> An: Nicholas M Glykos
> Cc: Norman Geist; Namd Mailing List
> Betreff: Re: namd-l: Sticking TIP4P water molecules AMBER
> can you tell us more on how you did prepare/generated your system?
> Did you use "set default FlexibleWater on" in tleap/xleap?
> See section 5 in this tutorial on how to use tip4p with amber ff in
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