[gmx-users] tunepme does not start

Wed Jun 18 01:08:16 CEST 2014

On Jun 17, 2014 11:35 PM, "Soren Wacker" <swacker at ucalgary.ca> wrote:
>
> Hi,
>
> I try to use mdrun with -tunepme. When I start it at a clusters login
node everything works fine. However, when I sent it to a cluster it seems
-tunepme gets ignored. mdrun is started and runs the tpr without tuning the
number of PME nodes. I attach an example script and a log file. Any idea
why this might happen?

mdrun -tunepme never changes the number of PME-only ranks. It can shift
load from reciprocal to real space, but only actually does so if there is
enough imbalance. As you can see at the end of your log file, the balance
is good for the number of PME ranks used.

Mark

> best regards
> Soren
>
> --
> Dr. Soeren Wacker
> Centre For Molecular Simulation, BI # 547
> The University of Calgary
> 2500 University Drive (NW)
> Calgary, Alberta
> Canada, T2N 1N4
>
> Tel.:   ++1 (403) 210 7860
> Email:  swacker at ucalgary.ca
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Chetan
Mahajan [chetanvm10 at gmail.com]
> Sent: Tuesday, June 17, 2014 3:20 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] peculiar water behavior
>
> Thanks, Justin. That makes it clear. I have one small question: I do not
> know how does position restraint algorithm work with other things in
> gromacs, but  doesn't it generate a lot of stress due to slab moving from
> center to near box boundary despite of position restraints, when -com
> option is used for refcoord-scaling? If there is a lot of stress, would
> this stress affect simulation results?
>
> Thanks and Regards,
> Chetan
>
>
> On Tue, Jun 17, 2014 at 10:01 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 6/17/14, 10:32 AM, Chetan Mahajan wrote:
> >
> >> Any ideas :
> >>
> >> 1. why slab is moving despite of position constraints?
> >>
> >>
> > Restraints are biasing potentials; they don't prevent movement.  Why is
it
> > necessary that your slab not move?
> >
> >
> >  2. That too, only with "com" option of refcoord scaling...with "all"
> >> option
> >> slab does not move...
> >>
> >>
> > Using "all" means the restraint reference for each atom is the original
> > position in the input coordinates, with respect to every atom
individually.
> >  It is more stringent, though it can often be unstable.  The "com"
option
> > means the restraint potential is calculated with respect to the COM of
the
> > group of restrained atoms; it is a bit more forgiving, since the COM
might
> > only move slightly, even if there are relatively larger changes in the
> > individual atomic positions.
> >
> > -Justin
> >
> >  Thanks
> >>
> >>
> >> On Sun, Jun 15, 2014 at 7:02 PM, Chetan Mahajan <chetanvm10 at gmail.com>
> >> wrote:
> >>
> >>  The pics should be seen in the reverse order. Due to sorting by name,
> >>> "After equilibration" pic occurs first.
> >>>
> >>>
> >>> On Sun, Jun 15, 2014 at 6:54 PM, Chetan Mahajan <chetanvm10 at gmail.com>
> >>> wrote:
> >>>
> >>>  Thanks.
> >>>>
> >>>> No, same things do not happen when it's a NVT simulation or no mixed
> >>>> potentials. Also, with mixed potentials in NPT simulation, this
things
> >>>> of
> >>>> slab moving in one direction (thus following water movement) happens
> >>>> only
> >>>> with -com option of refcoord-scaling, *not with -all option for
> >>>> refcoord-scaling. *
> >>>>
> >>>>
> >>>> I have a crystal slab with equal amount of water on both the sides.
> >>>> During NPT equilibration (with refcoord-scaling option of -com, not
> >>>> -all),
> >>>> some water on side side of the slab enters opposite side due to
periodic
> >>>> boundary conditions I have (say water on the right side of the slab,
> >>>> crosses boundary of the box and enter the left side of the slab due
to
> >>>> periodic boundaries. Even crystal slab follows this water and move
same
> >>>> distance in the same direction of water movement. Following link
shares
> >>>> pictures of the solvated slab before and after equilibration:
> >>>>
> >>>>
> >>>> https://www.dropbox.com/sh/tjq80jgnff1y7ur/AAAzhnv8uwl-UMQ0TYx8PuPAa
> >>>>
> >>>> I feel, this is not an error, but it is odd. Due to periodicity we
have,
> >>>> output of any calculations will remain the same.  Again, with -all
> >>>> option
> >>>> for refcoord scaling, this movement of water and slab DOES NOT occur.
> >>>>
> >>>> Thanks a lot!
> >>>> regards
> >>>> Chetan
> >>>>
> >>>>
> >>>> On Sat, Jun 14, 2014 at 4:40 AM, Mark Abraham <
mark.j.abraham at gmail.com
> >>>> >
> >>>> wrote:
> >>>>
> >>>>  Hi,
> >>>>>
> >>>>> Repeating myself - simplify things! Do sane things happen with NVT?
> >>>>> With
> >>>>> no
> >>>>> mixed potentials?
> >>>>>
> >>>>> Your words aren't making sense to me - you'll do much better with
> >>>>> pictures,
> >>>>> making sure you turn on your visualizer's option to show the
periodic
> >>>>> box.
> >>>>>
> >>>>> Mark
> >>>>>
> >>>>>
> >>>>> On Fri, Jun 13, 2014 at 8:45 PM, Chetan Mahajan <
chetanvm10 at gmail.com>
> >>>>> wrote:
> >>>>>
> >>>>>  Hi Justin,
> >>>>>>
> >>>>>> I, actually, do not want to preserve any voids. Initial void that I
> >>>>>> mentioned is supposed to be filled by water during equilibration
and
> >>>>>> it
> >>>>>> does so. However, problem is that some or major quantity of water
> >>>>>>
> >>>>> moves out
> >>>>>
> >>>>>> from one side of the box to enter from the opposite side (obeying
> >>>>>>
> >>>>> periodic
> >>>>>
> >>>>>> boundary conditions) and crystal slab moving following water
movement.
> >>>>>>
> >>>>> Thus
> >>>>>
> >>>>>> although initially there is almost equal amount of water on both
sides
> >>>>>>
> >>>>> of
> >>>>>
> >>>>>> the slab, we have more water on one side of the slab than the other
> >>>>>>
> >>>>> side
> >>>>>
> >>>>>> after equilibration. In other words, length of the box on one side
of
> >>>>>>
> >>>>> the
> >>>>>
> >>>>>> slab is more than the other side after equilibration, although it
is
> >>>>>>
> >>>>> same
> >>>>>
> >>>>>> on both sides before equilibration. My dilemma is whether this is
due
> >>>>>>
> >>>>> to
> >>>>>
> >>>>>> pressure coupling or any gromacs thing or due to potentials (mixed
> >>>>>> buckingham and LJ)?
> >>>>>>
> >>>>>> Thanks
> >>>>>> Chetan
> >>>>>>
> >>>>>>
> >>>>>> On Fri, Jun 13, 2014 at 7:43 AM, Justin Lemkul <jalemkul at vt.edu>
> >>>>>>
> >>>>> wrote:
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>>>
> >>>>>>> On 6/12/14, 11:15 PM, Chetan Mahajan wrote:
> >>>>>>>
> >>>>>>>  Dear All,
> >>>>>>>>
> >>>>>>>> I am simulating TiO2 crystal solvated by water  and ions like
> >>>>>>>>
> >>>>>>> sodium and
> >>>>>
> >>>>>> formate. I am observing one peculiar thing, and I would like to
> >>>>>>>>
> >>>>>>> rectify
> >>>>>
> >>>>>> that. I have initial structure of crystal slab at the center of the
> >>>>>>>>
> >>>>>>> box
> >>>>>
> >>>>>> elongated in z-direction and almost equal boxlength on both the
> >>>>>>>>
> >>>>>>> sides,
> >>>>>
> >>>>>> with
> >>>>>>>> a gap of 1 nm between slab surface and first layer of water
close to
> >>>>>>>>
> >>>>>>> slab.
> >>>>>>
> >>>>>>>    This space is kept to avoid water going on the sides of the
> >>>>>>>>
> >>>>>>> crystal
> >>>>>
> >>>>>> during
> >>>>>>>> equilibration. This was a minor information. Now, the main
> >>>>>>>>
> >>>>>>> observation
> >>>>>
> >>>>>> is
> >>>>>>
> >>>>>>> that during NPT equilibration, water from one side of the slab
> >>>>>>>>
> >>>>>>> enters
> >>>>>
> >>>>>> the
> >>>>>>
> >>>>>>> other opposite side of the slab (using periodic conditions) so
that
> >>>>>>>> boxlengths on both sides of the slab are very different at the
end
> >>>>>>>>
> >>>>>>> of
> >>>>>
> >>>>>> equilibration. Is this an artifact of pressure coupling? Following
> >>>>>>>>
> >>>>>>> is my
> >>>>>
> >>>>>> equilibration .mdp file. I have tried varying the compressibility
> >>>>>>>>
> >>>>>>> and
> >>>>>
> >>>>>> tau-p
> >>>>>>>> parameters in the following file. e.g. zero compressibility in
x/y
> >>>>>>>> direction or tau-p reduced to 3.
> >>>>>>>>
> >>>>>>>>
> >>>>>>> With pressure coupling, any voids present in the system will be
> >>>>>>> compressed.  If you need to try to preserve some sort of vacuum
> >>>>>>>
> >>>>>> layers,
> >>>>>
> >>>>>> use
> >>>>>>
> >>>>>>> NVT.
> >>>>>>>
> >>>>>>> -Justin
> >>>>>>>
> >>>>>>> --
> >>>>>>> ==================================================
> >>>>>>>
> >>>>>>> Justin A. Lemkul, Ph.D.
> >>>>>>> Ruth L. Kirschstein NRSA 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 | (410) 706-7441
> >>>>>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>>>>
> >>>>>>> ==================================================
> >>>>>>> --
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> >>>>>
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> >>>>>>>
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> >>>>
> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA 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 | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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