[gmx-users] gromacs.org_gmx-users Digest, Vol 156, Issue 48
Li, J.
jing.li at rug.nl
Thu Apr 13 10:29:35 CEST 2017
Hello, Justin, You were correct about the simulation box. I calculated the
simulation box again. I found the volume should be smaller just as your
suggestion. And now it works.
But I had found a question when I tried to find out how the memory was
allocated before I changed the box size. The memory should be
fourier-nx*fourier-ny*fourier-nz*4(for float type) byte, according to the
code. But number of the allocated elements are different between error
exhibition (3,425,307,227) and my calculation (110,592,000,000). The
difference is quite big. Do you know why?
By the way, changing fourierspacing can change the point for integration in
PME. But how pme-order works?
Thanks.
Jing
On Tue, Apr 11, 2017 at 2:44 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Lennard-Jones parameters for metal surfaces (Miguel Caro)
> 2. Re: Trying to use cutoff electrostatics with MARTINI
> (Mark Abraham)
> 3. Re: Error during nvt: Not enough memory. Failed to allocate
> 3425307227 aligned elements of size 4 for grid->grid. What is
> happening (Justin Lemkul)
> 4. Re: Heavy metals parameterisation (Justin Lemkul)
> 5. Re: how to know solvent molecule number (Justin Lemkul)
> 6. Re: Heavy metals parameterisation (Alex Mathew)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 11 Apr 2017 14:00:57 +0300
> From: Miguel Caro <miguel.caro at aalto.fi>
> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Lennard-Jones parameters for metal surfaces
> Message-ID: <3b1609e2-148b-afb9-3b31-799557e61ad2 at aalto.fi>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
>
> I want to run some simulations of water/metal interfaces, for which I
> need Lennard-Jones parameters optimized for the metallic atoms in the
> solid phase (e.g., opposite to as cations in solution). I know of the
> difficulty of correctly capturing the metal-water interaction with such
> a simple potential, but my idea was to run a Gromacs simulation with the
> OPLS force field to generate some *reasonable* initial input for ab
> initio MD.
>
> Since the OPLS force field supplied with Gromacs does not contain such
> parameters, I was wondering if someone could point me to relevant
> literature where I can find reliable and tested LJ parameters for
> transition metals. I'm initially testing with Ni but my idea is to run
> simulations for several other transition metals later on.
>
> I could of course parametrize the interactions myself from DFT
> calculations, but it seems a bit overkill at this stage. Any help would
> be much appreciated.
>
> Miguel
>
>
> --
> *Dr. Miguel Caro*
> /Postdoctoral researcher/
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: *mcaroba at gmail.com*
> Work: *miguel.caro at aalto.fi*
> Website: http://mcaroba.dyndns.org
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 11 Apr 2017 11:03:08 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Trying to use cutoff electrostatics with
> MARTINI
> Message-ID:
> <CAMNuMAR4GEkeib0H9JnFThV8=L5TYaKe9fHdEkV0oNnVoVLLhQ at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> On Tue, Apr 11, 2017 at 12:09 PM Graham J.A. <J.A.Graham at soton.ac.uk>
> wrote:
>
> > Hi,
> >
> > I'm preparing to do some benchmarking and wanted to look at the
> > performance differences between reaction-field and cutoffs for the
> > electrostatic model with the MARTINI forcefield.
> >
>
> You'd expect that to be small - one can implement plain cutoff as RF with a
> zero parameter.
>
>
> > I've downloaded the recommended MDPs from the MARTINI website, but when
> > I specify cutoff in the MDP I still get "NxN RF Elec. + LJ" in the
> > performance tables at the end of the log. The section at the top of
> > the log shows that GROMACS has recognised that I'm asking for cutoffs.
> >
> > This is happening with both GROMACS 2016.3 and 5.1.4. Am I
> > misunderstanding the log output, or is something going wrong?
> >
>
> Particularly on hardware that supports fused multiply-addition (most of the
> current relevant ones), the extra operation is ~free, and the only overhead
> is the load of the constant parameter, which happens outside the inner
> loop, and perhaps some register pressure. So we don't bother with a special
> kernel for this case, and your observations are expected.
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 11 Apr 2017 08:10:55 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error during nvt: Not enough memory. Failed
> to allocate 3425307227 aligned elements of size 4 for grid->grid.
> What
> is happening
> Message-ID: <74af0158-1890-8d3b-4cb0-9aa9c008af7c at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 4/10/17 8:12 AM, Li, J. wrote:
> > This error appeared when I tried to do a NVT simulation. The simulation
> box
> > is 768.00000 768.00000 768.00000 [nm**3], in which there are 90000 atoms.
>
> There's got to be a ton of void space in that system. 90,000 atoms should
> fill
> a box about 100,000 times smaller.
>
> Regardless, the memory allocation indicates that it needs 12 GB but can't
> have
> it, so you're just running out of memory. Either build a smaller system
> or use
> a machine with more memory.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 11 Apr 2017 08:11:51 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Heavy metals parameterisation
> Message-ID: <2a5ee511-916b-0bf2-2ae5-ebce0f111991 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 4/10/17 8:54 AM, Alex Mathew wrote:
> > Thanks Justin,
> >
> > I am looking for the effect of heavy metals in channel proteins. Could
> you
> > please provide me some links or paper to where i can start QMMM.
>
> That's a bit of a broad statement. If you're looking at something like
> transport through a channel, QM/MM may not be practical, depending on the
> resources available to you. But you can get yourself started with a simple
> Google search, and there are a number of good review articles.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 11 Apr 2017 08:12:39 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] how to know solvent molecule number
> Message-ID: <7aa44287-3ab5-4c8d-36bd-55fd6a453616 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 4/10/17 10:14 AM, Chintan Bhagat wrote:
> > Dear Justin,
> >
> > As You advised, I tried grep -c option
> >
> > My solvent file - ethanolamine.gro
> > PRODRG COORDS
> > 12
> > 1DRG OAC 1 -0.083 0.327 0.043
> > 1DRG HAE 2 -0.146 0.373 -0.019
> > 1DRG CAB 3 -0.074 0.188 0.009
> > 1DRG HAC 4 -0.172 0.143 0.025
> > 1DRG HAD 5 -0.037 0.178 -0.093
> > 1DRG CAA 6 0.022 0.117 0.105
> > 1DRG HAA 7 0.026 0.011 0.079
> > 1DRG HAB 8 -0.015 0.136 0.206
> > 1DRG NAD 9 0.158 0.174 0.097
> > 1DRG HAG 10 0.193 0.162 0.004
> > 1DRG HAH 11 0.217 0.125 0.161
> > 1DRG HAF 12 0.155 0.271 0.120
> > 0.53926 0.53926 0.53926
> >
> > So, I tried OAC as unique atom to count the number of ethanolamine
> (solvent
> > molecule) in my box.
> >
> > *lab1 at lab1-desktop:~/Desktop/md2$ grep -c OAC 1AKI_solv.gro10067*
> >
> > As i understand that my box is fully filled with 10067 ethanolamine
> > molecules which indicate this will be stimulation in 100% ethanolamine
> (if
> > I do further). If I want to do stimulation with 20% ethanolamine - 80%
> > water. Then, number of ethanolmine should come around 2013 molecule
> > (OAC=2013) in 1AKI_solv.gro file.
> >
> > Is it correct?
> >
>
> Yes.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 11 Apr 2017 18:14:09 +0530
> From: Alex Mathew <alexmathewmd at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Heavy metals parameterisation
> Message-ID:
> <CAAW-8xUK7PVmJEGP=C8uQQotXfsYZ3YsGnT5vQdqNrxYWNQiWQ at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Justin,
> More specifically, I'm looking for the transport properties of proteins in
> presence and absence of heavy metals- how heavy metals affecting the
> transportation of molecules across the channels.
>
>
> ------------------------------
>
> --
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> End of gromacs.org_gmx-users Digest, Vol 156, Issue 48
> ******************************************************
>
--
Jing Li
PhD student
FMNS, University of Groningen
Room 5115.0309, Nijenborg 4, Groningen
The Netherlands
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