From: Bowman, Jacob (bowman.1334_at_buckeyemail.osu.edu)
Date: Tue Jul 09 2019 - 09:52:34 CDT
The order of the atoms for the waters is O H1 H2 EPW. The masses of the lone pairs is set to 0. Rigidbonds is set for all. I think that I was missing the definition of the water model! I add the flag watermodel with tip4pew and it fixed my error!
Thank you so much for the help! I appreciate it
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From: Peter Freddolino <petefred_at_umich.edu>
Sent: Tuesday, July 9, 2019 10:24:44 AM
To: <namd-l_at_ks.uiuc.edu>; Bowman, Jacob
Subject: Re: namd-l: EPW "ATOMS Moving too fast"
could you please check a few quick things?
First, what is the ORDER of the atoms in your prmtop file for each water?
Second, what are the masses of the lone pair atoms in your prmtop file?
Third, what are the settings that you are using for rigidbonds and watermodel?
On Mon, Jul 8, 2019 at 5:14 PM Bowman, Jacob <bowman.1334_at_buckeyemail.osu.edu<mailto:bowman.1334_at_buckeyemail.osu.edu>> wrote:
I am currently using NAMD with Amber to run a simulation of a protein/ligand complex in an octahedral water box with TIP4Pew water model.
The initial structure comes from the end of a previous simulation that is provided by a tutorial for the program SEEKR.
Then I am able to run a minimization for the water molecules over 5000 steps, with the protein/ligand atoms fixed.
When I move on to a temperature equilibration stage, I run into the error:
Atoms moving too fast - and they are all exclusively the EPW atoms.
I have run the minimization for longer and tried to reduce the temperature on the temperature equilibration to no avail.
Is there any way to overcome this issue? I have tried this same scheme with the TIP3P model and it works just fine. I'm not sure where the error with the TIP4Pew is coming from.
OSBP Graduate Student
Department of Chemistry and Biochemistry
2116 Newman Wolfrom
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