[gmx-users] Energy Minimize problem about converge!!

[Erik Wensink]

hi,
cavities/voids in the system -system far from equilibruim density-
can also result in potential energy >0. Carrying out  MD runs with high 
pressure -after
first doing steepest descents- can 'drive these voids' out out and bring 
the systeem closer to an equilibrium configuration (still normal md 
required after, to reach this).
best regards,
Erik

nanyu101 wrote:

>Dear gmx-users,
>  When I run energy minimize,my system told me that it can converge.And my starting structure is formal.It's the information that system told:
>Steepest Descents:
>   Tolerance         =  1.00000e+02
>   Number of steps   =       250000
>
>Stepsize too small (9.79552e-07 nm)Converged to machine precision,
>but not to the requested precision (100)
>
>writing lowest energy coordinates.
>
>Steepest Descents did not converge in 32 steps
>  Potential Energy  =  1.49787e+04
>Maximum force:  1.35434e+03
>
>My em.mdp is below;
>;
>;	User spoel (236)
>;	Wed Nov  3 17:12:44 1993
>;	Input file
>;
>cpp                 =  /lib/cpp
>define              =  -DFLEX_SPC
>constraints         =  none
>integrator          =  steep
>emtol               =  10
>emstep              =  0.02
>nsteps              =  50000
>nstcgsteep          =  1000
>pbc                 =  xyz
>nstxout             =  500
>nstvout             =  500
>nstlog              =  500
>nstlist             =  10
>ns_type             =  grid
>rlist               =  1.0
>rcoulomb            =  1.0
>rvdw                =  1.0
>tcoupl              =  no
>Pcoupl              =  Berendsen
>tau_p               =  1.0
>compressibility     =  4.5e-5
>ref_p               =  1.0
>gen_vel             =  yes
>gen_temp            =  500
>gen_seed            =  173529
>
>
>Was it wrong?If it's right,are there possible my topology file wrong or my force field wrong,such as proper and improper dihedrals,angles and bonds? Thanks for your help.
>
>Best wishes,
>Xianhui Wu
>______________________________________
>
>===================================================================
>Ãâ·ÑÊÔÓÃÐÂÀË15MÈÎÄãÓÊ »ñÊýÂëÏà»ú¡¢ÊÖ»ú´ó½± (http://vip.sina.com/sol_mail/promotion/pro_men.html)
>ÐÂÀ˶þÊÖÊг¡£ºÒ»ÔªÍ¶È룬ʮ·Ö¾ªÏ²£¬°Ù·ÖÂúÒâ (http://classad.sina.com.cn/2shou/)
>ÊýÍòÕÅÊÖ»úͼƬÊýÍòÊ׶ÌÐÅÁåÉùÈÎÄãÌôÑ¡£¬Ã¿Ì춼ÓиüР(http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi)
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>
>  
>

-- 
Erik Wensink                 Phone:  +47-55-582850
Fysisk institutt, Rm.496     GSM:    +46-70-4950676
University of Bergen         Fax:    +47-55-589440
Allegt. 55                   E-mail:
N-5007 Bergen, NORWAY        erikw at fi.uib.no