Abhishek Banerjee wrote:
Hi all,
Thanks a lot for your reply. Actually I will tell you
the problem. I want a binary mixture of DMF and methanol. Then I want to
study the self diffusion coefficient as function of mole fraction of ant
of the component. Now I got a reference about DMF. They used CS2 model
with six interaction sites of DMF. So I took all the parameters and
wrote a separate itp file.
#ifdef _FF_OPLS
[ atomtypes ]
;type mass charge ptype sigma epsilon
CH3 15.0350 0.280 A 3.80000e-01 8.00000e+01
N 14.0067 -0.570 A 3.20000e-01 8.00000e+01
C 12.0110 0.570 A 3.70000e-01 5.00000e+01
O 15.9994 -0.500 A 2.96000e-01 1.00000e+02
H 1.0008 0.060 A 2.20000e-01 8.00000e+00
#endif
[ moleculetype ]
; Name nrexcl
DMF 3
#ifdef _FF_OPLS
[ atoms ]
; nr type resnr resid atom cgnr charge
1 CH3 1 DMF C1 1 0.280
2 N 1 DMF N 1 -0.570
3 CH3 1 DMF C2 1 0.280
4 C 1 DMF C 1 0.570
5 O 1 DMF O 1 -0.500
6 H 1 DMF H 1 0.060
#endif
"dmf.itp" 42L, 1288C
Now my question is how do i make a solvent box of DMF with this itp
file. Plz help
An .itp file contains parameters, not coordinates, so you cannot use it to
create your box. You need a coordinate file. Aside from that, I gave you some
ideas about the commands you need to generate a mixture using genbox in the last
post.
-Justin
thanx
abhishek
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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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