[gmx-users] Re:united atom

[Justin Lemkul]

On 2/7/13 10:43 AM, Ali Alizadeh wrote:
> Dear Justin
>
> Thank you for your reply,
>
> I want to use Nose-Hoover thermostat and MTTK barostat and shake
> algorithm and md-vv integrator,
>
> but I got this error:
>
> -----------------------------------
> Fatal error:
> SHAKE is not supported with domain decomposition and constraint that
> cross charge group boundaries, use LINCS
> --------------------------------------
>

Then clearly your combination of parameters is unsupported.  Do as the error 
message says, or perhaps trying running using particle decomposition (mdrun 
-pd), which will be slower than DD.

-Justin

> A part of my topology file:
> ------------------
> [ moleculetype ]
> ; Name            nrexcl
> DECANE                  9
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
> ; residue   0 LI  rtp LI   q  0.0
>       1   opls_071      0     LI     C1      1          0     14.027   ; qtot 0
>       2   opls_071      0     LI     C2      2          0     14.027   ; qtot 0
>       3   opls_071      0     LI     C3      3          0     14.027   ; qtot 0
>       4   opls_071      0     LI     C4      4          0     14.027   ; qtot 0
>       5   opls_071      0     LI     C5      5          0     14.027   ; qtot 0
>       6   opls_071      0     LI     C6      6          0     14.027   ; qtot 0
>       7   opls_068      0     LI     C7      7          0     15.035   ; qtot 0
>       8   opls_071      0     LI     C8      8          0     14.027   ; qtot 0
>       9   opls_068      0     LI     C9      9          0     15.035   ; qtot 0
>      10   opls_071      0     LI    C10      10          0     14.027   ; qtot 0
>
> -------------------------------
>
>
> On 2/7/13 9:46 AM, Ali Alizadeh wrote:
>> Dear All user
>>
>> There are 350 decane molecules in my simulation box,
>>
>> I like doing a simulation(npt ensemble) by a united atom force field,
>> Can I use the opls (nonbonded: L-J 6-12 and coloumb) that is in
>> gromacs?
>>
>> Beside, How can I neglect  coloumb interaction(non-bonded) and
>> dihedrals(bonded)?
>>
>
>>> The OPLS force field in Gromacs contains both OPLS-AA (all-atom) and OPLS-UA
>>> (united-atom) types, so you could in theory use OPLS-UA, but that's a fairly
>>> ancient force field.  In that case, there are no Coulombic interactions anyway,
>>> because the united-atom carbons should not have any charge.  If you want to
>>> neglect dihedrals, I think you're hacking the force field in a way that makes no
>>> sense.
>
>>> -Justin
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================