[gmx-users] Energy minimisation problem

[silvester.thu]

I guess you have not listed all the dihedrals in the configuration of a ethanol molecule.
In your .top file, there are only two dihedrals, you might need to include all others.
By the way, check the other part of your topology to avoid other incorrect inputs.

Best regards.

Yue Shao 





silvester.thu
2008-05-14



发件人： Jussi Lehtola
发送时间： 2008-05-14 11:28:31
收件人： Discussion list for GROMACS users
抄送： 
主题： RE: [gmx-users] Energy minimisation problem


On  Tue,  2008-05-13  at  20:32  +0300,  Jussi  Lehtola  wrote:
>  On  Tue,  2008-05-13  at  14:34  +0100,  Kukol,  Andreas  wrote:
>   >  First  try  the  EM/MD  of  1  molecule  in  vacuum  ('ethanol-gas')  and  check,  if  it  looks  reasonable.
>   >  
>  Thanks,  using  the  vacuum  method  I  seem  to  get  better  results.

It  seems  I  spoke  too  soon.  Energy  minimising  the  one-particle  structure
in  vacuum  gives  me  the  following  potential  energies:

methanol 21.4
ethanol 9.4
propanol 3.8
butanol 4.1
pentanol 12.2
hexanol 81.0

All  minimizations  have  converged  with  Fmax   <  1e-3.  Are  these  energies
reasonable?  The  energies  of  methanol  and  hexanol  are  somewhat  high.

Energy  minimisation  with  a  system  of  4913  methanol  molecules  with
initial  density  of  500  kg/m^3  and  periodic  boundary  conditions  gives  as
potential  energy  Epot  =  -1.67e5,  however  the  forces  do  not  converge.  
Running  the  system  with  Berendsen  pressure  and  temperature  thermostats
(p  =  1  bar,  T  =  300  K)  results  in  a  crash  after  82  ps.  The  total  energy
is  positive  and  of  the  order  1e5.
--  
------------------------------------------------------
Jussi  Lehtola,  FM,  Tohtorikoulutettava
Fysiikan  laitos,  Helsingin  Yliopisto
jussi.lehtola at helsinki.fi,  p.  191  50673
------------------------------------------------------
Mr.  Jussi  Lehtola,  M.  Sc.,  Doctoral  Student
Department  of  Physics,  University  of  Helsinki,  Finland
jussi.lehtola at helsinki.fi
------------------------------------------------------

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