[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

[Justin A. Lemkul]

Pablo Englebienne wrote:
> OK, I started over with the CHCl3 box from scratch. I prepared the 
> following itp file from the CHCL3 parameters in ffG53a5.rtp:
> 
> ---[chcl3.itp]---
> [ moleculetype ]
> ; Name            nrexcl
> CHCL3             3
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
>     1       HCHL      1  CHCL3   HChL      1      0.082      1.008       
> 2       CCHL      1  CHCL3   CChL      1      0.179     12.011      
> 3      CLCHL      1  CHCL3  CLCh1      1     -0.087     35.453     
> 4      CLCHL      1  CHCL3  CLCh2      1     -0.087     35.453     
> 5      CLCHL      1  CHCL3  CLCh3      1     -0.087     35.453
> 
> [ bonds ]
> ;  ai    aj funct               1     2     2    gb_39
>    2     3     2    gb_40
>    2     4     2    gb_40
>    2     5     2    gb_40
>    1     3     2    gb_47
>    1     4     2    gb_47
>    1     5     2    gb_47
>    3     4     2    gb_48
>    3     5     2    gb_48
>    4     5     2    gb_48
> 
> [ angles ]
> ;  ai    aj    ak funct             1     2     3     2  ga_43
>    1     2     4     2  ga_43
>    1     2     5     2  ga_43
>    3     2     4     2  ga_44
>    3     2     5     2  ga_44
>    4     2     5     2  ga_44
> ---[chcl3.itp]---
> 
> I noticed that G53a5 includes 4 types of bond stretching terms specific 
> for CHCl3 (C-Cl, C-H, H-Cl and Cl-Cl), therefore I specified all of 
> them. Should all of these terms be harmonic bonds (function type 2) or 
> some (e.g., the H-Cl and Cl-Cl terms) should be type 6 (as described in 
> section 5.4 of the manual)? I tried with both types and I get the same 
> minimized structure with the following topology and mdp files:
> 

The bonds defined correspond with what I get when I run pdb2gmx on a chloroform 
molecule, so I would suspect you have them properly defined as function type 2, 
although pdb2gmx defines many more angles and even dihedrals, probably given the 
weird bonding setup in CHCl3.  I don't know how that might affect your system.

I also discovered a minor bug in the Gromos96 .rtp files in the CHCl3 directive 
- no bond is defined between C and H.  Will file a bugzilla.

-Justin

> ---[topol.top]---
> ; Include forcefield parameters
> #include "ffG53a5.itp"
> #include "chcl3.itp"
> 
> [ system ]
> ; Name
> Chloroform
> 
> [ molecules ]
> ; Compound        #mols
> CHCL3             1
> ---[topol.top]---
> 
> ---[em.mdp]---
> integrator          =  cg
> nsteps              =  50000
> ;
> ;    Energy minimizing stuff
> ;
> emtol               =  1e-5
> emstep              =  0.01
> 
> ;
> ;    Electrostatics
> ;
> coulombtype         =  cut-off
> rcoulomb            =  0
> ns_type             =  simple
> nstlist             =  0
> rlist            =  0
> 
> ;
> ;    vdW
> ;
> rvdw                =  0
> 
> ;
> ;       PBC
> ;
> pbc            =  no
> ---[em.mdp]---
> 
> In the minimized structure, not all C-Cl distances are equivalent, 
> although the minimization converges OK.
> 
> Any comments?
> 
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-- 
========================================

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

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