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