From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Wed Oct 24 2012 - 15:31:58 CDT
Yep, that was set properly. I'm not sure given my very limited (and thus far unsuccessful) use of tip4, but I think if you leave out FlexibleWater the simulation doesn't run at all…
From: Jesper Sørensen <jesorensen_at_ucsd.edu<mailto:jesorensen_at_ucsd.edu>>
Date: Wed, 24 Oct 2012 15:00:07 -0500
To: Aron Broom <broomsday_at_gmail.com<mailto:broomsday_at_gmail.com>>
Cc: "namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>>
Subject: Re: namd-l: unreasonably high temp/pressure. .
You probably did this but just in case:
When you generated your prmtop did you set "set default FlexibleWater on" in LEaP?
http://ambermd.org/namd/namd_amber.html, section 5
On Oct 24, 2012, at 8:26 AM, Aron Broom <broomsday_at_gmail.com<mailto:broomsday_at_gmail.com>> wrote:
Did you tell NAMD you are using TIP4P? you have to put "waterModel tip4" in your config file, the default is tip3.
On Wed, Oct 24, 2012 at 10:55 AM, Martin, Erik W <Erik.Martin_at_stjude.org<mailto:Erik.Martin_at_stjude.org>> wrote:
I'm hoping someone on this list will have some insight on this problem I've been having. I'm running a simulation of an 82aa peptide in a truncated octahedron water box for a total of ~100k atoms. I'm also using an AMBER ff. I have been running this simulation for ~25ns using tip3 water with no problems at all. However, I wanted to run this with tip4 water as well and am seemingly incapable of getting it to equilibrate properly.
On the first structure, I was able to equilibrate it by constraining peptide coordinates and allowing the water – with rigid bonds – to equilibrate in the cell. When I rebuilt the system with tip4 water I did absolutely nothing different. It runs fine with rigid bonds on and the peptide constrained, but when I try to allow it to run I get the dreaded "atoms moving too fast" error at about step 120-200. It is different atoms every time, and what seems to be happening is that the temperature and pressure both ramp up to enormous values. (for the record, I'm using Langevin dynamics to control temp and pressure)
Does anyone have a clue what could be causing this condition?
Thanks a lot,
Email Disclaimer: www.stjude.org/emaildisclaimer<http://www.stjude.org/emaildisclaimer>
Consultation Disclaimer: www.stjude.org/consultationdisclaimer<http://www.stjude.org/consultationdisclaimer>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:42 CST