[gmx-users] Choosing LINCS setting / rcon for parallel mdrun
Agnivo Gosai
agnivogromacs14 at gmail.com
Mon Nov 16 19:49:21 CET 2015
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.
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:
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> 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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