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

Ben Tam btam125 at hotmail.co.uk
Fri Jul 8 19:01:41 CEST 2016 

To follow on with that I have another question, this is the error I am keep getting when I turn on pressure couple (and now too with pressure couple off) :


WARNING: Listed nonbonded interaction between particles 41 and 133
at distance 4.169 which is larger than the table limit 2.000 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

The question means, does this mean my force field is not good or my crystal topology is not great? I convert my crystal file (.cif) by converting it to (.pdb) and using x2top function to convert it to .top file.



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 17:17
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme



On 7/8/16 12:05 PM, Ben Tam wrote:
> Dear all,
>
>
> My systems size is:
>
>
>     2.58730   2.24067   2.06100
>
>
> And I am not using a pressure coupling, furthermore I did not input
> periodic_molecules = yes
>
> Henceforth, should I just make the system bigger? at the moment I am simulating just 574 molecules.
>

First try to run without DD (e.g. mdrun -ntmpi 1 as I suggested) to make sure
your topology is sound.  Then, if it's useful, try increasing the size of the
system.  It would be useful to determine why DD is trying to assign such large
bonded interactions, though.  But your system is too small to really benefit
from DD, anyway.

-Justin

> 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 Justin Lemkul <jalemkul at vt.edu>
> Sent: 08 July 2016 16:30
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem with Group and Verlet cut -off scheme
>
>
>
> On 7/8/16 10:54 AM, Ben Tam 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.
>>
>>
>
> Are your molecules infinite, e.g. bonded across PBC by using "periodic_molecules
> = yes"?  If so, that would probably explain it.
>
> But the bigger issue is that your system may be too small to be efficiently
> parallelized via DD.  You're probably going to be losing performance.  Your
> smallest vector is 2 nm, but what are the other vectors?  Is the system cubic?
> You can also try -ntmpi 1 and using OpenMP only for parallelization.  Also note
> that if you're using pressure coupling, you may have lots of minimum image
> violations, depending on what the other box vectors are.
>
>> By the way, do I reply to the gmx-user at gromacs.org address or how do I reply without disturbing other users?
>>
>
> Reply to that address to send to the list.  Support is provided by the
> community, not any one specific person, and the open posting of problems and
> solutions helps everyone (and fills a useful archive).
>
> -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.
>
>
>
>
> ==================================================
> --
> 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.
>

--
==================================================

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

==================================================
--
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.

More information about the gromacs.org_gmx-users mailing list