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

Fri Jul 8 19:41:34 CEST 2016

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
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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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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