Em 05/04/2015 14:44, Jashimuddin Ashraf jashimuddin.ashra...@gmail.com
escreveu:
Dear gromacs users,
I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create
an equilibrated structure of SO2 molecules using the gmx insert-molecules
function. As I try to minimize the energy of the system, I always get
this-
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax 10 (which may not be possible for your system).
It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way,
we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
That isn't necessarily a problem here, unless the maximum force is too
high. You have requested a low threshold (emtol =10) and the machine
precision can't reach it on simple precision.
I tried to analyze my .gro file that the gmx insert-molecules function is
returning me and found that some of my SO2 have a bond in between them. Is
this what causes the energy minimization to crash?
Also, the .gro file just outputs atoms coordinates. There is no 'bonds' on
it. Usualy, that is a visualization problem.
Is there any way I can
prepare an equilibrated system of liquid SO2 ?
Yes. Read the paper 'Force field benchmark for organic liquids' and you
might get an idea how to do it.
My SO2.itp file is like this (I made this an .itp because I wish to study
this system along with some other molecules)-
[ moleculetype ]
; Name nrexcl
SO23
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeBchargeB massB
1 opls_202 1 SR S 1 0.6512 32.07
;qtot 0.6512
2 opls_326 1 SR O1 2-0.3256 15.99940
;qtot 0.3256
3 opls_326 1 SR O2 3-0.3256 15.99940
; qtot 0
; opls_202 S 16 32.07 0.6512 A3.61500e-01 1.2125232
; opls_326 O 8 15.99940-0.3256 A3.00500e-01 0.47756176
[ bonds ]
; aiaj functc0c1c2c3
1 2 1 0.1434 635968.0
1 3 1 0.1434635968.0
[ distance_restraints ]
; aiaj type index type' low up1 up2 fac
1 2 1 0 1 1.149 1.490 1.490 1.0
1 3 1 0 1 1.149 1.490 1.490 1.0
[ angles ]
; aiajak functc0c1
c2c3
2 1 3 1119.51359.8
I have also uploaded the .gro file that the gmx insert-molecules function
is returning me after this text.
SO2_box300.gro
https://docs.google.com/file/d/0B8p1k0KkNddyUEN3dzZRZE5keXM/edit?usp=drive_web
Thanks in advance.
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