[gmx-users] Re:united atom

[ABEL Stephane 175950]

Hello, 

Is it correct for you that in your topolgy file, some atoms have wrong  mass (i.e. C7 and C9 have a mass of 15.035 instead of 14.027) in your DECAN  molecule ? Are they at the end ? 

Stephane 


------------------------------

Message: 3
Date: Thu, 7 Feb 2013 19:13:11 +0330
From: Ali Alizadeh <ali.alizadehmojarad at gmail.com>
Subject: [gmx-users] Re:united atom
To: gmx-users <gmx-users at gromacs.org>
Message-ID:
        <CAPfUHmvnBU3v0VErKO_faXUvKk0QTg7HGazAtjp16-a1RShY9A at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

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
--------------------------------------

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

--
Sincerely

Ali Alizadeh
University of Tehran
College of engineering(Fanni)
Department of chemical engineering
IPE (Institute of Petroleum Engineering)
M.Sc Candidate, class of 2013
B.Sc Graduate 2011(University of Tehran,Fanni)