[gmx-users] Minimization problem, again!

[andrea spitaleri]

Hi
I had a similar problem with protein/membrane system and I found that 
the starting structure was wrong. Precisly, there were few clashes 
between atoms of the protein with the membrane. Once removed them, the 
min worked fine.
I hope this can help,
Regards

Andrea

liu xin wrote:

> Dear GROMACS users,
>
> My minizization problem still got no resolvment, even I restarted from 
> make hole, using different values for "hfm", I got almost the same 
> message when I try to minimize my lipid/protein system.  so I send 
> this mail again asking for help.
>
> I checked the output energy, after SD minimization with my 
> lipid/protein system, found the values are abnormal:
>
> ##########################################################################
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 2000.
> Potential Energy  =            nan
> Maximum force     =            inf on atom 9614
> Norm of force     =            nan
> ##########################################################################
>
> Then I checked the em.log line by line, found there are two message:
>
> ##########################################################################
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 2000
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> ##########################################################################
>
> Infact I did set "constraints = none" in mdp file, and I got the same 
> result when changing the stepsize from 0.002 to 0.02. I searched this 
> forum, somebody said it is because of bad start structure, so I 
> restarted from makeing hole, using hfm = 5, 10, 10 then 100, 100, 150, 
> but I still got almost the same result, except that the atom number of 
> "Maximum force" varies, I am new to gromacs, I've been stuck into this 
> problem for a week, could anybody give me some suggestions? Any 
> suggestions will be highly appriciated!
>
> Thanks in advance!
>
>------------------------------------------------------------------------
>
>_______________________________________________
>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.
>

-- 
-------------------------------
Andrea Spitaleri
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Get Firefox! <http://www.spreadfirefox.com/?q=affiliates&id=0&t=85>
-------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051215/42fc06d3/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: firefox_80x15.png
Type: image/png
Size: 1063 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051215/42fc06d3/attachment.png>