[gmx-users] Choosing LINCS setting / rcon for parallel mdrun
Mark Abraham
mark.j.abraham at gmail.com
Mon Nov 16 20:11:17 CET 2015
Hi,
On Mon, Nov 16, 2015 at 7:50 PM Agnivo Gosai <agnivogromacs14 at gmail.com>
wrote:
> Dr. Lemkul
>
> Thanks for your reply.
> However , I used npme = 0 and could then utilize 64 processes. I did a NPT
> equilibration with Berendsen thermostats / barostats and found after 5 ns
> the density to be 999 kg/cu m and average press = 0.4 bar. There was
> marginal drift.
> Are these artifacts or I need to equilibrate more ? I used AMBER99SB/TIP3P.
>
Probably, since you've used barostat and thermostat that do not define a
correct ensemble, and don't know what your error estimate for your
quantities is :-) You should also decide in advance what you are planning
to observe, and your decision about what to regard as an equilibration
criterion needs to relate to that.
Mark
> Thanks & Regards
> Agnivo Gosai
> Grad Student, Iowa State University.
>
> On Mon, Nov 16, 2015 at 1:49 AM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
>
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> > Today's Topics:
> >
> > 1. Re: Problems with trjconv (Shantanu Maheshwari)
> > 2. Choosing LINCS setting / rcon for parallel mdrun (Agnivo Gosai)
> > 3. Re: Choosing LINCS setting / rcon for parallel mdrun
> > (Justin Lemkul)
> > 4. difference between entropic energy and free energy (Ming Tang)
> > 5. (no subject) (Mehriar Amininasab)
> >
> >
> > ---------- Forwarded message ----------
> > From: Shantanu Maheshwari <shantanu256 at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc:
> > Date: Mon, 16 Nov 2015 00:30:10 +0100
> > Subject: Re: [gmx-users] Problems with trjconv
> > No it will not erase anything from .trr file.
> >
> > On Mon, Nov 16, 2015 at 12:21 AM, Mishelle Oña <samimishu at hotmail.com>
> > wrote:
> >
> > > Ok, but this erase the frame from my trajectory? because i don´t want
> to
> > > modify it.
> > >
> > > > Date: Mon, 16 Nov 2015 00:10:07 +0100
> > > > From: shantanu256 at gmail.com
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] Problems with trjconv
> > > >
> > > > If you want to take out only one frame then you can use -dump option.
> > > >
> > > > trjconv -f trajcentrada.trr -dump 1646 -o 1646ps.gro
> > > >
> > > > On Sun, Nov 15, 2015 at 11:39 PM, Mishelle Oña <
> samimishu at hotmail.com>
> > > > wrote:
> > > >
> > > > > Yes, but I am not converting all the .trr file to gro I wanted to
> > take
> > > > > only one frame of the .trr and make it gro. That´s why my command
> is
> > > > > trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro
> > > > > if the command line above is wrong :( what is the command I should
> > use
> > > for
> > > > > taking out only one frame of a trajectory file in gro format
> > > > > Mishelle
> > > > >
> > > > > > From: mark.j.abraham at gmail.com
> > > > > > Date: Sun, 15 Nov 2015 22:06:38 +0000
> > > > > > To: gmx-users at gromacs.org
> > > > > > Subject: Re: [gmx-users] Problems with trjconv
> > > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Your question had one-word answer, which I gave! :-) If the size
> > of
> > > your
> > > > > > files is worth thinking about, then converting them to gro format
> > is
> > > not
> > > > > a
> > > > > > great idea.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Sun, 15 Nov 2015 21:56 Mishelle Oña <samimishu at hotmail.com>
> > > wrote:
> > > > > >
> > > > > > > Eh, I don´t understand what you mean, please explain me
> > > .Mishelle:)
> > > > > > >
> > > > > > > > From: mark.j.abraham at gmail.com
> > > > > > > > Date: Sun, 15 Nov 2015 19:28:47 +0000
> > > > > > > > To: gmx-users at gromacs.org
> > > > > > > > Subject: Re: [gmx-users] Problems with trjconv
> > > > > > > >
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > Certainly. You do not want to convert non-trivial
> trajectories
> > to
> > > > > text
> > > > > > > > format.
> > > > > > > >
> > > > > > > > Mark
> > > > > > > >
> > > > > > > > On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña <
> > > samimishu at hotmail.com>
> > > > > > > wrote:
> > > > > > > >
> > > > > > > > > well, I check and it is the same line of command. The
> biggest
> > > file
> > > > > has
> > > > > > > > > more weight than the .traj file and it is only a .gro file
> .
> > Is
> > > > > this
> > > > > > > > > posible?
> > > > > > > > > Mishelle
> > > > > > > > > > From: mark.j.abraham at gmail.com
> > > > > > > > > > Date: Sun, 15 Nov 2015 19:15:50 +0000
> > > > > > > > > > To: gmx-users at gromacs.org
> > > > > > > > > > Subject: Re: [gmx-users] Problems with trjconv
> > > > > > > > > >
> > > > > > > > > > Hi,
> > > > > > > > > >
> > > > > > > > > > Either you didn't issue the same command (inspect your
> > > terminal
> > > > > > > history),
> > > > > > > > > > or the second operation didn't complete (for any number
> of
> > > > > reasons).
> > > > > > > > > >
> > > > > > > > > > Mark
> > > > > > > > > >
> > > > > > > > > > On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña <
> > > > > samimishu at hotmail.com>
> > > > > > > > > wrote:
> > > > > > > > > >
> > > > > > > > > > > Hello, I have a question about trjconv. I have a .trr
> > file
> > > and
> > > > > I
> > > > > > > put
> > > > > > > > > the
> > > > > > > > > > > following line of command: trjconv -f trajcentrada.trr
> -b
> > > 1646
> > > > > -e
> > > > > > > 1646
> > > > > > > > > -o
> > > > > > > > > > > 1646ps.gro I got back a file of 13813272703 bytes.
> Then I
> > > make
> > > > > the
> > > > > > > > > same and
> > > > > > > > > > > got a file of 506444 bytes. Do you know what is
> > > > > happening?Mishelle
> > > > > > > > > > > --
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> >
> >
> >
> > ---------- Forwarded message ----------
> > From: Agnivo Gosai <agnivogromacs14 at gmail.com>
> > To: gmx-users at gromacs.org
> > Cc:
> > Date: Sun, 15 Nov 2015 19:09:19 -0600
> > Subject: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun
> > Dear Users,
> >
> > I tried to do a NVT run on a cluster with -np = 64. My system size is
> 12405
> > atoms ( a protein in water )
> >
> > I get the following error.
> >
> > ERROR.
> >
> > There is no domain decomposition for 56 nodes that is compatible with the
> > given box and a minimum cell size of 0.959375 nm
> > Change the number of nodes or mdrun option -rcon or -dds or your LINCS
> > settings
> >
> > 8 nodes were assigned for PME cal by mdrun
> >
> > This is the part of my NVT.mdp
> >
> > ; Bond parameters
> > continuation = no ; first dynamics run
> > constraint_algorithm = lincs ; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> > constrained
> > lincs_iter = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 5 ; 10 fs
> > rlist = 1.4 ; short-range neighborlist cutoff (in nm)
> > rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
> > rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
> > ; Electrostatics
> > coulombtype = PME ; Particle Mesh Ewald for long-range
> > electrostatics
> > pme_order = 4 ; cubic interpolation
> > fourierspacing = 0.12 ; grid spacing for FFT
> >
> > I would still like to use 64 processes for the mdrun. Any suggestions
> > please.
> >
> > I am thinking of playing with -rcon. But I am not sure if it will affect
> > the accuracy of the simulation.
> >
> > Thanks & Regards
> > Agnivo Gosai
> > Grad Student, Iowa State University.
> >
> >
> >
> > ---------- Forwarded message ----------
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Cc:
> > Date: Sun, 15 Nov 2015 20:14:27 -0500
> > Subject: Re: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun
> >
> >
> > On 11/15/15 8:09 PM, Agnivo Gosai wrote:
> >
> >> Dear Users,
> >>
> >> I tried to do a NVT run on a cluster with -np = 64. My system size is
> >> 12405
> >> atoms ( a protein in water )
> >>
> >> I get the following error.
> >>
> >> ERROR.
> >>
> >> There is no domain decomposition for 56 nodes that is compatible with
> the
> >> given box and a minimum cell size of 0.959375 nm
> >> Change the number of nodes or mdrun option -rcon or -dds or your LINCS
> >> settings
> >>
> >> 8 nodes were assigned for PME cal by mdrun
> >>
> >> This is the part of my NVT.mdp
> >>
> >> ; Bond parameters
> >> continuation = no ; first dynamics run
> >> constraint_algorithm = lincs ; holonomic constraints
> >> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> >> constrained
> >> lincs_iter = 1 ; accuracy of LINCS
> >> lincs_order = 4 ; also related to accuracy
> >> ; Neighborsearching
> >> ns_type = grid ; search neighboring grid cells
> >> nstlist = 5 ; 10 fs
> >> rlist = 1.4 ; short-range neighborlist cutoff (in nm)
> >> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
> >> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
> >> ; Electrostatics
> >> coulombtype = PME ; Particle Mesh Ewald for long-range
> >> electrostatics
> >> pme_order = 4 ; cubic interpolation
> >> fourierspacing = 0.12 ; grid spacing for FFT
> >>
> >> I would still like to use 64 processes for the mdrun. Any suggestions
> >> please.
> >>
> >>
> > Your system is too small to decompose over 64 cores. One cannot
> > arbitrarily parallelize any system over any number of cores/nodes.
> >
> > -Justin
> >
> > I am thinking of playing with -rcon. But I am not sure if it will affect
> >> the accuracy of the simulation.
> >>
> >> Thanks & Regards
> >> Agnivo Gosai
> >> Grad Student, Iowa State University.
> >>
> >>
> > --
> > ==================================================
> >
> > 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
> >
> > ==================================================
> >
> >
> >
> > ---------- Forwarded message ----------
> > From: Ming Tang <m21.tang at qut.edu.au>
> > To: "gromacs.org_gmx-users at maillist.sys.kth.se" <
> > gromacs.org_gmx-users at maillist.sys.kth.se>
> > Cc:
> > Date: Mon, 16 Nov 2015 03:20:21 +0000
> > Subject: [gmx-users] difference between entropic energy and free energy
> > Deer list,
> >
> > I am quite confused about the concept of entropic energy and free energy.
> > Could anybody help to tell me what is the difference between them?
> >
> > Thanks.
> >
> >
> >
> > ---------- Forwarded message ----------
> > From: Mehriar Amininasab <Amininasab at khayam.ut.ac.ir>
> > To: gmx-users at gromacs.org
> > Cc:
> > Date: Mon, 16 Nov 2015 11:12:14 +0330
> > Subject: [gmx-users] (no subject)
> > Dear gromacs users,
> >
> > Does anybody have an idea about the value of isothermal compressibility
> at
> > kbar pressures.
> >
> > yours,
> > Mehriar
> >
> >
> > --
> > Gromacs Users mailing list
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