From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Wed Oct 24 2012 - 10:34:57 CDT
Yep. I did set that. It does seem to have something to do with the water though given that the problem arises when I turn rigid bonds off. If it helps, I'll attach one of my configuration files… There might be some odd values there though given that I started changing some things to try to rectify the problem (margin and cutoff distances etc)
From: Aron Broom <broomsday_at_gmail.com<mailto:broomsday_at_gmail.com>>
Date: Wed, 24 Oct 2012 10:26:43 -0500
To: Erik Martin <erik.martin_at_stjude.org<mailto:erik.martin_at_stjude.org>>
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
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,
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-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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