This is an error when using Amber for simulations.
The exact error message is:
"ERROR: Atom 13272 velocity is -3401.72 -6060.9 7670.82 (limit is 8000, atom 134 of 191 on patch 138 pe 7)"
But This error is for nearly all of the EPW "atoms" in the simulation.
I'll try the simulation without the ligand as well.
Thanks,
Jacob
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Monday, July 8, 2019 1:29:40 PM
To: AMBER Mailing List
Subject: Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW
Can you clarify what you mean by "NAMD with Amber"? Is this a NAMD error,
or when you use Amber for simulations?
I would also see if the problem occurs without the ligand; often errors can
be a sign of issues with user defined force field parameters.
On Mon, Jul 8, 2019, 1:25 PM Bowman, Jacob <bowman.1334.buckeyemail.osu.edu>
wrote:
> Hello Amber Users,
>
>
> 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. TLEAP is used with this file:
>
> "source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.protein.ff14SB
> source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.gaff
> source /path/.conda/envs/conda_seekr5/dat/leap/cmd/leaprc.water.tip4pew
> set default FlexibleWater on
> set default PBRadii mbondi2
> loadoff /path/SEEKR/Tutorial/Ca2.lib
> loadoff /path/SEEKR/Tutorial/benzamidine.lib
> loadamberparams /path/SEEKR/Tutorial/benzamidine.frcmod
> WAT= T4E
> HOH= T4E
> loadAmberParams
> /path/.conda/envs/conda_seekr5/dat/leap/parm/frcmod.ionsjc_tip4pew
> loadAmberParams /path/.conda/envs/conda_seekr5/dat/leap/parm/frcmod.tip4pew
>
> holo = loadpdb
> /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/holo_wet.pdb
>
> bond holo.7.SG holo.137.SG
> bond holo.25.SG holo.41.SG
> bond holo.109.SG holo.210.SG
> bond holo.116.SG holo.183.SG
> bond holo.148.SG holo.162.SG
> bond holo.173.SG holo.197.SG
> charge holo
> check holo
>
> saveamberparm holo
> /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/building/holo2.parm7
> /path/SEEKR/Tutorial/root_dir/anchor_2_2_site1_-1.1_19.6_18.3_0/md/building/holo2.rst7
>
> savepdb holo /path/holo_leap.pdb
>
> quit
> "
>
> I get the note:
>
> Note: 1-4: angle 23026 23027 duplicates bond ('triangular' bond) or angle
> ('square' bond)
> For nearly all the water molecules.
>
> Then I am able to run a minimization for the water molecules 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.
>
>
>
> Jacob Bowman
>
> OSBP Graduate Student
>
> Lindert Lab
>
> Department of Chemistry and Biochemistry
>
> 2116 Newman Wolfrom
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 08 2019 - 11:00:02 PDT
