[gmx-users] Structuring as function of z - gmx order

Tue Sep 2 04:00:25 CEST 2014

I have a system that contains a constrained crystal molecules plus free molecules and water.  What I would like to obtain is a measure of the structuring of the free molecules as a function of the z direction across the box.

Using GROMACS 5.0

First attempt I tried using gmx h2order, however appears that unless atom names are oxygen/hydrogen it does not generate the data.  Works fine for the water in the system, but when go to non-water, output is zeros only.

Next tried using gmx order.  I can get it to generate the order parameter (S) with respect to the z axis as a function of the z distance fine (using -os -sl 100), as well as x axis-x direction and y axis-y direction (using -d x and -d y).

However, what I would like is to have the values for Sx, Sy and Sz as a function of distance across the box in the z direction (i.e. within slices taken across the x-y plane).  Sz can get fine, and that does tell me something about the ordering of the molecules.  However, since that is only relative to one axis, that is not the entire story.

Using -noszonly with -os generates the Sx, Sy, Sz values; but only in the -o output file (overall/average value?), the -os file is not generated.

Using -szonly will generate the order parameter per slice in the direction specified by -d, as noted above.

Should the script be generating the order parameter relative to all three axis along a particular axis direction when -noszonly is specified?

Or is there an alternative scrip that someone could suggest to use?

Thank you for any suggestions and input.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> Mark Abraham
> Sent: Tuesday, 2 September 2014 2:29 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Segmentation fault mdrun
> 
> Hi,
> 
> For example, Martini's webpages don't claim 40fs is universally
> applicable,
> so I'd be thinking in that direction... Perhaps you can increase the
> time
> step after you equilibrate, but just as with atomistic simulations, you
> might need to be more gentle while you are equilibrating. Also, your
> tau-t
> is on the short side for that time step.
> 
> Mark
> 
> 
> On Mon, Sep 1, 2014 at 5:26 PM, Alex s <as1783 at hotmail.com> wrote:
> 
> >
> >
> >
> > They're ions that I've just added to the water phase of the system.
> That
> > was a case I highlighted to show how sensitive the system is to minor
> > changes. I have other systems which are ion free and still experience
> > segmentation fault.
> > I've just reviewed all my md runs for my systems, I have found that 2
> of
> > the systems which experienced segmentation fault had a warning that
> the
> > pressure scaling was more than 1 %  . However the other systems that
> > experienced segmentation fault presented no such warning yet the
> force
> > imbalance was as high as 6 %. Could this be the issue?
> > Thanks
> > Alex
> >
> > > Date: Sun, 31 Aug 2014 17:14:48 -0400
> > > From: jalemkul at vt.edu
> > > To: gmx-users at gromacs.org
> > > Subject: Re: [gmx-users] Segmentation fault mdrun
> > >
> > >
> > >
> > > On 8/31/14, 1:55 PM, Alex s wrote:
> > > >
> > > > There was a typo in the last message, I found NO issues in point
> 2.
> > >
> > > Actually, you did.  You said when you removed the ions, the problem
> was
> > > resolved.  That indicates to me that the ions are somehow unstable.
> I
> > don't
> > > know much about doing CG simulations, so maybe someone else can
> advise,
> > but it
> > > seems that the long time step is causing large forces to accumulate
> on
> > the ions
> > > and you get the crash.  Are the ion particles just a single ion or
> some
> > > representation of a hydrated ion?
> > >
> > > -Justin
> > >
> > > > From: as1783 at hotmail.com
> > > > To: gmx-users at gromacs.org
> > > > Date: Sun, 31 Aug 2014 18:52:39 +0100
> > > > Subject: Re: [gmx-users] Segmentation fault mdrun
> > > >
> > > > Thanks for the reply
> > > > I've attached a copy of my mdp file. It is a coarse grained
> system so
> > a time step of 0.04 shouldn't be a problem. Regarding the link you've
> > given, points 1 and 4 are not applicable to my situation, I've tried
> point
> > 2 and found issues. What should I be looking for in point 3?
> > > > Thanks
> > > > Alex
> > > >> Date: Sun, 31 Aug 2014 13:20:31 -0400
> > > >> From: jalemkul at vt.edu
> > > >> To: gmx-users at gromacs.org
> > > >> Subject: Re: [gmx-users] Segmentation fault mdrun
> > > >>
> > > >>
> > > >>
> > > >> On 8/31/14, 1:17 PM, Alex s wrote:
> > > >>> Hi
> > > >>> I'd really appreciate some advice on this issue, I tend to get
> a
> > segmentation fault during my mdrun. I've searched online for ways to
> > resolve this and tried to diagnose whats causing this problem but I'm
> > having no luck.
> > > >>> I know that if you get a segmentation fault at step 0 its most
> > likely a problem with system configuration or a minimization issue.
> However
> > for my system I successfully run energy minimization and
> equilibration.
> > When I run md the segmentation fault occurs usually very late on the
> system
> > (past the 100ns mark).
> > > >>> I've found that minor adjustments to the system can either lead
> to
> > the error or remove it. For example for one system, I ran it ION free
> and I
> > had no issues, however when I just replace 12 water molecules with
> NA+ and
> > CL- this leads to a segmentation fault. Also I was able to fix this
> error
> > in another system just by changing the time step from to 0.04 to
> 0.03.
> > > >>>   From what I'm describing, does it seem as if the fault lies
> with
> > the system set up? or the mdp file? or could it be a compiler issue?
> What
> > information should I be looking for in my output file to perhaps
> determine
> > where issue lays?
> > > >>
> > > >> Provide the full .mdp file and people can comment on it.  Is
> this an
> > atomistic
> > > >> system?  A time step of 0.04 is insane if it is.
> > > >>
> > > >> Diagnostics:
> > > >>
> >
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_
> an_Unstable_System
> > > >>
> > > >> -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
> > > >>
> > > >> ==================================================
> > > >> --
> > > >> Gromacs Users mailing list
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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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