[gmx-users] Problem with Group and Verlet cut -off scheme

Mark Abraham mark.j.abraham at gmail.com
Fri Jul 8 23:51:50 CEST 2016 

Hi,

OK. A "[pairs]" interaction is a bonded interaction... so don't do that
unless you need to (and probably alongside other bonded interactions
involved). If you want a non-bonded interaction, you should not be
specifying things in the topology. Non-bonded interactions are
intrinsically spatial, apart from what nrexcl specifies.

Perhaps you'd do best to fully describe the model physics you'd like to
implement :-)

Mark

On Fri, Jul 8, 2016 at 7:41 PM Ben Tam <btam125 at hotmail.co.uk> wrote:

> Hi Mark,
>
>
> Sorry I don't think I fully understand what you are saying. Am I correct
> that you are implying not to have bonded parameter for the crystal?
>
>
> Thank you for your suggestions and I have already done that, by that I
> means just using normal force field and I managed to get the crystal
> working. What I am doing now is trying to add a pair interaction into the
> working crystal and force field through tabulation of table (due to mixing
> lennard jones and buckingham potential) and I am new to it. Therefore
> apologies for any fundamental questions.
>
>
> Best regards,
>
>
> Ben
>
>
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: 08 July 2016 18:16
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme
>
> Hi,
>
> Why does your topology have any bonded interactions if you are simulating a
> crystal and want to play with interactions?
>
> Also I strongly encourage you to get a normal crystal working before you
> think about tables. Then normal with tables. Then modified tables.
>
> Mark
>
> On Fri, 8 Jul 2016 16:55 Ben Tam <btam125 at hotmail.co.uk> wrote:
>
> > Hi Justin,
> >
> >
> > This is what I got from the log file:
> >
> >
> > Initializing Domain Decomposition on 6 ranks
> > Dynamic load balancing: auto
> > Will sort the charge groups at every domain (re)decomposition
> > Initial maximum inter charge-group distances:
> >     two-body bonded interactions: 4.882 nm, Bond, atoms 456 457
> >   multi-body bonded interactions: 4.915 nm, Angle, atoms 457 459
> > Minimum cell size due to bonded interactions: 5.407 nm
> > Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> > Optimizing the DD grid for 6 cells with a minimum initial size of 6.758
> nm
> > The maximum allowed number of cells is: X 0 Y 0 Z 0
> >
> >
> >
> > But when I check, this the atoms that is limiting (from .gro file) :
> >
> >
> >     1MOL     C1  455   0.728   1.339   1.541
> >     1MOL     C2  456   0.696   1.224   1.636
> >     1MOL     C3  457   0.737   1.220   1.769
> >     1MOL     C4  458   0.692   1.112   1.851
> >     1MOL     H4  459   0.713   1.112   1.951
> >
> >
> > And non of them tells me they are over 4nm, which I am not sure where
> else
> > it could go wrong. The smallest length of my box is 2 nm and my cut-off
> > length is 1 nm. Thank you for your help.
> >
> >
> > By the way, do I reply to the gmx-user at gromacs.org address or how do I
> > reply without disturbing other users?
> >
> >
> > Thank you again,
> >
> >
> > Ben
> >
> >
> > ________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin
> > Lemkul <jalemkul at vt.edu>
> > Sent: 08 July 2016 15:22
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme
> >
> >
> >
> > On 7/8/16 10:20 AM, Ben Tam wrote:
> > > Hi Mark,
> > >
> > >
> > > It shouldn't, what I am simulated is a crystal structure and my
> > tabulated forcefield is only up to 3nm. Do you think the problem is
> there?
> > To avoid the charge group, I am putting in the section of [atoms]:
> > >
> > >
> > > [ atoms ]
> > > ;   nr       type  resnr residue  atom   cgnr     charge       mass
> > typeB    chargeB      massB
> > > 1 Mg 1 MOL Mg 1
> > > 2 O1 1 MOL O1 2
> > > 3 O2 1 MOL O2 3
> > > 4 O3 1 MOL O3 4
> > > .        .      .         .             .       .
> > >
> > > .        .      .         .             .       .
> > >
> > > .        .      .         .             .       .
> > >
> > >
> > > ... etc.
> > >
> > >
> >
> > The DD setup section of the .log file will tell you exactly what the
> > limiting
> > interactions are.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > 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
> [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<
> http://mackerell.umaryland.edu/~jalemkul>
>
> Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul>
> mackerell.umaryland.edu
> Welcome to my site! To learn more about me and the work I am doing, please
> use the navigation links above.
>
>
>
> > [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<
> > http://mackerell.umaryland.edu/~jalemkul>
> >
> > Justin A. Lemkul - MacKerell Lab<
> http://mackerell.umaryland.edu/~jalemkul>
> > mackerell.umaryland.edu
> > Welcome to my site! To learn more about me and the work I am doing,
> please
> > use the navigation links above.
> >
> >
> >
> >
> > ==================================================
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