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