Dave, All Amber Users,
Thank you for your response. I am doing NPT equilibration with one NVT phase, and I will recheck the protocol one more time.
However, it appears to me now that the solution is trivial, but I'd like to make sure that I have really fixed the problem,
not just make it look like a normal MD behavior.
1. The input PDB file (from the PDB database) names all the magnesium ions MG
2. In my LEaP script I also had to call "addIons mol MG 0" to add 14 neutralizing magnesiums because the call from
the tutorial "addIons mol Mg2+ 0" yielded an error.
3. In parmed input script, I had a call "add12_6_4 .%Mg2+ watermodel TIP3P"
Oddly, It did not generate any errors.
4. I changed the above to "add12_6_4 .%MG watermodel TIP3P" to match the PDB file and LEaP commands.
Now, since neither of the parmed calls ( from 3. or 4.) issued any errors, is what I just did truly correct, and am I running
my seemingly normal-looking MD with the intended Li & Mertz 12_6_4 parameters, as opposed to falling back onto
some defaults? I would appreciate some feedback on the above. Why did "addIons mol Mg2+ 0" really fail in LEaP,
while "addIons mol Na+ 0" is fine?
Also, I want to run the same RNA with neutralizing MGs and additional Na+ and Cl- pairs.
Should I use frcmod.ions1lm_126_tip3p with frcmod.ions234lm_1264_tip3p?
Thank you in advance for clarifications and advice,
Voytek Kasprzak
Wojciech (Voytek) K. Kasprzak (Contractor)
Bioinformatics Analyst
Basic Science Program
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537
kasprzaw.mail.nih.gov
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: David Cerutti [dscerutti.gmail.com]
Sent: Thursday, December 6, 2018 3:32 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+
You need to run your equilibration in NPT. The solvent is contracting
around itself to minimize surface area like water would on the Space
Station. I'm not sure where the error is coming from--it's a very common
symptom of many things that can go wrong, but probably some particle has
somehow gotten accelerated to very high speed and the arithmetic gets
broken. The contraction you're seeing is going to happen in all systems
depending on how much vacuum space is initially present, and the artifact
is really a coalesced, more regular shaped vacuum bubble tiled with the
water / biomolecule. Because the box size is going to change under NPT,
you'll need to use the CPU version of the code at the start. Start with
minimization and a small timestep, then switch on NPT, and see how things
go.
Dave
On Thu, Dec 6, 2018 at 3:21 PM Kasprzak, Wojciech (NIH/NCI) [C] <
wojciech.kasprzak.nih.gov> wrote:
>
> Dear Amber Users,
>
> I have attempted an Amber 18 PME run for an RNA fragment with multiple
> Mg2+ ions (X-ray data) which I
> neutralized with additional magnesiums. Following Amber tutorial
> "Modeling a Magnesium-DNA System using
> the 12-6-4 LJ-Type Nonbonded Model" (
> http://ambermd.org/tutorials/advanced/tutorial20/12_6_4.htm#ref3),
> I built the PRMTOP and INPCRD files via LEaP and ParmEd, as follows:
>
> 1) LEaP:
> source leaprc.RNA.OL3
> source leaprc.water.tip3p
> loadamberparams frcmod.ions234lm_1264_tip3p
>
> mol=loadpdb RNA-7MG.pdb
> check mol - net charge of
> -28
> addIons mol MG 0 - I had to use MG;
> Mg2+ led to an error in LEaP
> check mol
> savepdb mol 2NOK_nionsMG.pdb
>
> solvateBox mol TIP3PBOX 10.0 0.832
> savepdb mol RNA7MG-solvMG.pdb
> saveAmberParm mol 2RNA7MG-solvMG.prmtop RNA7MG-solvMG.inpcrd
> quit
>
> 2) ParmEd:
> loadRestrt RNA7MG-solvMG.inpcrd
> setOverwrite True
> add12_6_4 .%Mg2+ watermodel TIP3P
> outparm RNA7MG-solvMG-1264.prmtop RNA7MG-solvMG-1264.inpcrd -
> *CCOEF section added to PRMTOP
>
> Following the above, I started an equilibration run (repeated MIN, HEAT,
> MD at 300K phases with slowly released harmonic restraints,
> calling pmemd.cuda and pmemd.cuda.MPI binaries). Very quickly, beginnning
> with the first heating for 40ps, the solvent box begins to
> distort in a periodic way I have never seen before in runs with monovalent
> ions.
>
> Please, refer to the attached PNG file (my earlier e-mail with 3 PDBs was
> too large for posting unfortunately) as the system's shape is
> hard to describe. I hope that this pattern of 8 spherical voids around
> the original cuboid box will remind somebody of a problem they
> have seen before.
>
> While the MD terminates with errors (cudaMemcpy GpuBuffer:: Download
> failed an illegal memory access was encountered), probably
> due to expanding size of the system, the RNA and the Mg ions stay close
> with three of them maintaining correct coordinating positions.
>
> I have tested Amber 18 PME system with TIP3P waters and default Na+/Cl-
> ions, and it behaves correctly.
>
> Hope to hear advice on how to fix the problem or how to debug the issue.
> Best regards, Voytek Kasprzak
>
> Wojciech (Voytek) K. Kasprzak (Contractor)
> Bioinformatics Analyst
> Basic Science Program
> Frederick National Laboratory for Cancer Research
> Leidos Biomedical Research, Inc.
> Post Office Box B
> Frederick, Maryland 21702
> Phone: 301-846-5537
> kasprzaw.mail.nih.gov
> http://binkley2.ncifcrf.gov/users/kasprzak
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Dec 06 2018 - 14:00:03 PST
