[gmx-users] exclusions

[Steven Neumann]

Thanks, I will apply harmonic bonds with whatever force constant then.
Would that speed up the performance with all exclusions and bonds?
Does the increase of the force constant in posre.itp make the simulation
slower? I used Fx=Fy=Fz=30 000

Steven


On Thu, Dec 5, 2013 at 5:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/5/13 11:50 AM, Steven Neumann wrote:
>
>> Thanks I did it. However I got an error:
>>
>> Invalid order for directive exclusions
>>
>> My topology:
>>
>> [ defaults ]
>> ; nbfunccomb-rule    gen-pairs    fudgeLJ    fudgeQQ
>> ....
>>
>> [ atomtypes ]
>> ;name    at.num    mass    charge    ptype    C6    C12
>> .....
>>
>>
>> ; Include Tube topology
>> #include "tube.itp"
>>
>> ; Include Position restraint file of ligand
>> #ifdef POSRES_TUB
>> #include "posre_tube.itp"
>> #endif
>>
>>
>> [ system ]
>> ; Name
>> Protein
>>
>> [ molecules ]
>> ; Compound        #mols
>> TUBE             1
>>
>>
>> whre tube.itp
>>
>> [ moleculetype ]
>> ; Name            nrexcl
>> TUBE             3
>>
>> [ atoms ]
>> ;   nr       type  resnr residue  atom   cgnr     charge       mass
>> typeB    chargeB      massB
>> ; residue   1 TUB rtp TUB  q  0.0
>> .....
>>
>>
>>
>> [ exclusions ]
>> .....
>>
>>
>> I do not have any bonds dihedrals or angles...
>>
>>
> That's an essential piece of information that you hadn't shared yet.
>  Exclusions are based on bonded geometry.  If you don't have bonds,
> exclusions won't work. If there are no bonds, the only option is
> energygrp-excl, otherwise you need to define bonds between the beads.  If
> the configuration is fully restrained, then the bonded parameters should
> matter very little.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==================================================
> --
> 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.
>