[gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 10
William Welch
wwelch000 at gmail.com
Fri Feb 7 01:40:40 CET 2014
I'm not sure if I'm replying correctly, but I just wanted to mention that I
would love to file a report to the redmine list, but I have not been
approved to do so. Is there another place I can report this problem?
Will
On Mon, Feb 3, 2014 at 2:35 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: multiple GPU on multiple nodes (Szil?rd P?ll)
> 2. Re: question (Thomas Piggot)
> 3. Annealing doesn't work with Andersen thermostat? (William Welch)
> 4. Re: Annealing doesn't work with Andersen thermostat?
> (Michael Shirts)
> 5. intel GPU acceleration? (Albert)
> 6. Re: intel GPU acceleration? (Tamas Horvath)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 3 Feb 2014 20:36:30 +0100
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] multiple GPU on multiple nodes
> Message-ID:
> <
> CANnYEw6u_34+0dXZTc5e-KM3+Uc6SKvLUw6pm53iH4AxZ97LDw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Sat, Feb 1, 2014 at 12:06 AM, cyberjhon <cyberjhon at hotmail.com> wrote:
> > Hi Szilard
> >
> > Thanks for your answer but I think that I did not make myself clear
> enough
> >
> > I am trying to use 2 GPUs, each one in a different node.
> > but it seems that gromacs only detects the one.
>
> How do you know that it only detects one?
>
> The message which says "1 GPU detected on host nid00900:" does not
> mean that only one GPU was detected. The log file is written on a
> single rank (master rank = #0) and that's where you get the detection
> output. The GPU setup is assumed to be homogenous across nodes, i.e.
> if on node nid00900 you have one GPU and you run two PP ranks on it
> (-gpu_id 00) this will mean that on another rank, e.g. nid00901, the
> same setup will apply.
>
> Cheers,
> --
> Szil?rd
>
> >
> > When I submit the job, I ask for two nodes, and the two nodes are being
> > given.
> > but the gromacs gpu version only is detecting one and one GPU.
> >
> > Do you know any way to make that it detects both nodes and therefore both
> > GPUs ?
> >
> > Thanks
> >
> > John Michael
> >
> >
> >
> > --
> > View this message in context:
> http://gromacs.5086.x6.nabble.com/multiple-GPU-on-multiple-nodes-tp5014085p5014203.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
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> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 3 Feb 2014 19:38:03 +0000
> From: Thomas Piggot <t.piggot at soton.ac.uk>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] question
> Message-ID: <52EFF01B.2060801 at soton.ac.uk>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>
> I guess the force field to use is a bit down to choice, however I would
> say that there are several force fields which should not be used in this
> case. There are several force fields/parameterisations that do not
> behave well for these two types of lipids (e.g. many Berger based
> parameters). As suggested, a thorough search through the literature is
> really what you need to do (e.g. for PG
> http://pubs.acs.org/doi/abs/10.1021/jp900645z ; for both (and apologies
> for the self promotion) the supp info from
> http://pubs.acs.org/doi/abs/10.1021/jp207013v and many more papers that
> are out there). For making a choice between force fields you should
> weigh up things like accuracy, speed of simulation, lipid diffusion
> rates, inclusion of other components of your system (e.g. proteins,
> etc.) and so on.
>
> Cheers
>
> Tom
>
> On 02/03/2014 07:06 PM, Justin Lemkul wrote:
> >
> >
> > On 2/3/14, 2:03 PM, nafas wrote:
> >> Hi
> >> thanks for your help.
> >> I think charmm force field imust use.but i dont know who can i found
> >> its files ?
> >>
> >
> > The full CHARMM36 force field in Gromacs format can be obtained from
> > http://mackerell.umaryland.edu/CHARMM_ff_params.html.
> >
> > -Justin
> >
> >>
> >> On Monday, February 3, 2014 9:19 PM, Justin Lemkul <jalemkul at vt.edu>
> >> wrote:
> >>
> >>
> >> On 2/3/14, 12:30 PM, nafas wrote:
> >> > Hi
> >> > I am tring with mixture pope/popg for simulatie membrane bacteria
> >> that i use
> >> of gromos53a6 force field.
> >> > what force field should i use?charmm force field?
> >> >
> >>
> >> What does your scrutiny of the literature tell you? Which force
> >> field succeeds
> >> in the most meaningful ways?
> >>
> >>
> >> > in program have been used pope.itp ,popg.itp, .....files .
> >> > I want to run grompp command but give afatall error:not found NH3L
> >> atomtype.
> >> > grompp -f minim.mdp -c ......gro -p ....top -o em.tpr
> >> >
> >> > I dont know what is problem?
> >>
> >>
> >> You have not constructed the force field correctly. Without
> >> significantly more
> >> detail, there's nothing useful to suggest beyond a thorough read
> >> through Chapter
> >> 5 of the manual.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 601
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu
> >> <mailto:jalemkul at outerbanks.umaryland.edu> |
> >> (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >>
> >> ==================================================
> >>
> >>
> >
>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 3 Feb 2014 13:02:27 -0700
> From: William Welch <wwelch000 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Annealing doesn't work with Andersen thermostat?
> Message-ID:
> <
> CAEy4365XycLRK+phHuin7jv1V96ps2++cg4xvh+cjae4v2O4+A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> I am doing some simulations on simple Lennard-Jones spheres and course
> grained hydrocarbon models. I have been using the annealing utility
> successfully until I switched from the V-rescale thermostat to the Andersen
> thermostat. When I use the Andersen thermostat, the system gets to the
> first temperature and then stays there. This does not happen if I switch to
> a different thermostat. My guess is that Andersen not available with
> annealing, at least in the version I'm using (4.6) , however I have not
> been able to find any reference to that online or in the mailing list. Here
> is one of the mdp files that produced a simulation that did not work. .
>
> title = 8pore
> integrator = md-vv
> dt = 0.003 ; ps !
> nsteps = 2500000 ; total 7500 ps.
> nstcomm = 1
> nstxout = 2000
> nstvout = 2000
> nstfout = 0
> nstlog = 100
> nstenergy = 1
> nstlist = 10
> ns_type = grid
> rlist = 1.5
> rcoulomb = 1.5
> rvdw = 1.5
> ; Berendsen temperature coupling is on in two groups
> Tcoupl = Andersen
> tc-grps = LJ BL
> tau_t = 0.1 0.1
> ref_t = 230 230
> ; Energy monitoring
> energygrps = LJ BL
> energygrp-excl = BL BL
> freezegrps = BL
> freezedim = Y Y Y
> ; Isotropic pressure coupling is now on
> ;Pcoupl = berendsen
> ;Pcoupltype = isotropic
> ;tau_p = 0.5
> ;compressibility = 4.5e-5
> ;ref_p = 1.0
> annealing = single single
> annealing-npoints = 20 20
> annealing-time = 0 200 400 800 1200 1600 2000 2400 2800 3200 3600
> 4000 4400 4800 5200 5600 6000 6400 6800 7200 0 200 400 800 1200 1600 2000
> 2400 2800 3200 3600 4000 4400 4800 5200 5600 6000 6400 6800 7200
> annealing-temp = 100 200 230 240 250 260 270 280 290 300 310 320 330
> 340 350 360 370 380 390 400 100 200 230 240 250 260 270 280 290 300 310 320
> 330 340 350 360 370 380 390 400
> ;Generate velocites is off at 300 K.
> gen_vel = yes
> gen_temp = 230.0
> ;gen_seed = 173529
>
> Velocities are generated at 230 (which is kind of strange, but changing
> that doesn't do anything) and the system cools to 100K and then stays
> there. The output in the md.log file shows that the correct ref_t is being
> read, but the actual temperature of the system does not increase. The same
> input using the md integrator and the V-rescaling thermostat does what it's
> supposed to.
> Will
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 3 Feb 2014 15:52:06 -0500
> From: Michael Shirts <mrshirts at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Annealing doesn't work with Andersen
> thermostat?
> Message-ID:
> <CA+zJb=gfrqK9WDBgFvw2Hy6mhba5=
> 484nxW+d4v1Vf6ifE6PyA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi, William-
>
> Interesting. There's too many conditionals with the current patchwork
> of temperature control methods, so there is an ongoing (though too
> slow) effort to reorganize the algorithms to eliminate such errors as
> this.
>
> For a medium-term solution, I'd suggest filing a redmine issue
> (redmine.gromacs.org) on this error so that it gets fixed for the next
> round of update.
>
> In the short-term, if you are interested in introducing stochasticness
> into the annealing, I'd suggest using the sd integrator for now.
>
> On Mon, Feb 3, 2014 at 3:02 PM, William Welch <wwelch000 at gmail.com> wrote:
> > Hi,
> > I am doing some simulations on simple Lennard-Jones spheres and course
> > grained hydrocarbon models. I have been using the annealing utility
> > successfully until I switched from the V-rescale thermostat to the
> Andersen
> > thermostat. When I use the Andersen thermostat, the system gets to the
> > first temperature and then stays there. This does not happen if I switch
> to
> > a different thermostat. My guess is that Andersen not available with
> > annealing, at least in the version I'm using (4.6) , however I have not
> > been able to find any reference to that online or in the mailing list.
> Here
> > is one of the mdp files that produced a simulation that did not work. .
> >
> > title = 8pore
> > integrator = md-vv
> > dt = 0.003 ; ps !
> > nsteps = 2500000 ; total 7500 ps.
> > nstcomm = 1
> > nstxout = 2000
> > nstvout = 2000
> > nstfout = 0
> > nstlog = 100
> > nstenergy = 1
> > nstlist = 10
> > ns_type = grid
> > rlist = 1.5
> > rcoulomb = 1.5
> > rvdw = 1.5
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl = Andersen
> > tc-grps = LJ BL
> > tau_t = 0.1 0.1
> > ref_t = 230 230
> > ; Energy monitoring
> > energygrps = LJ BL
> > energygrp-excl = BL BL
> > freezegrps = BL
> > freezedim = Y Y Y
> > ; Isotropic pressure coupling is now on
> > ;Pcoupl = berendsen
> > ;Pcoupltype = isotropic
> > ;tau_p = 0.5
> > ;compressibility = 4.5e-5
> > ;ref_p = 1.0
> > annealing = single single
> > annealing-npoints = 20 20
> > annealing-time = 0 200 400 800 1200 1600 2000 2400 2800 3200 3600
> > 4000 4400 4800 5200 5600 6000 6400 6800 7200 0 200 400 800 1200 1600
> 2000
> > 2400 2800 3200 3600 4000 4400 4800 5200 5600 6000 6400 6800 7200
> > annealing-temp = 100 200 230 240 250 260 270 280 290 300 310 320
> 330
> > 340 350 360 370 380 390 400 100 200 230 240 250 260 270 280 290 300 310
> 320
> > 330 340 350 360 370 380 390 400
> > ;Generate velocites is off at 300 K.
> > gen_vel = yes
> > gen_temp = 230.0
> > ;gen_seed = 173529
> >
> > Velocities are generated at 230 (which is kind of strange, but changing
> > that doesn't do anything) and the system cools to 100K and then stays
> > there. The output in the md.log file shows that the correct ref_t is
> being
> > read, but the actual temperature of the system does not increase. The
> same
> > input using the md integrator and the V-rescaling thermostat does what
> it's
> > supposed to.
> > Will
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 3 Feb 2014 21:56:25 +0100
> From: Albert <mailmd2011 at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] intel GPU acceleration?
> Message-ID:
> <
> CAO2eAcuOpzoBv4kaVmw5EbZVaC2xhUc_pRRxq9vvipXU1N-qqw at mail.gmail.com>
> Content-Type: text/plain; charset=GB2312
>
> Hello?
>
> I noticed that Intel also have GPU such as: Intel(R) Xeon Phi(tm)
> coprocessor
> 3120A. I am just wondering is the latest version of Gromacs support such
> kind of GPU calculation?
>
> thank you very much.
>
> Albert
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 3 Feb 2014 22:35:27 +0100
> From: Tamas Horvath <hotafin at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] intel GPU acceleration?
> Message-ID:
> <
> CAFNqVghxugeG88aLb549vsQmcv_yy7AmELOB8cngxtXt67r9Vg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> It's actually more like a cluster on a card than a gpu. It has x86 cores
> (albeit very simple ones). Theoretically any x86 code compiled with the
> xeon phi compiler can run on it without any further modification, though
> further optimizations are possible.
>
>
> On 3 February 2014 21:56, Albert <mailmd2011 at gmail.com> wrote:
>
> > Hello?
> >
> > I noticed that Intel also have GPU such as: Intel(R) Xeon Phi(tm)
> > coprocessor
> > 3120A. I am just wondering is the latest version of Gromacs support such
> > kind of GPU calculation?
> >
> > thank you very much.
> >
> > Albert
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
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> posting!
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>
> End of gromacs.org_gmx-users Digest, Vol 118, Issue 10
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