From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Jul 09 2019 - 09:24:44 CDT
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
On Mon, Jul 8, 2019 at 5:14 PM Bowman, Jacob <
> Hello all,
> 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.
> Thank you,
> Jacob Bowman
> OSBP Graduate Student
> Lindert Lab
> Department of Chemistry and Biochemistry
> 2116 Newman Wolfrom
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