[gmx-users] about "LINCS WARNING"

zhang ray zhangray7823 at msn.com
Tue Jan 21 03:22:44 CET 2003

Thank you Anton Feenstra, Kun-Lin Yang, and all gmx-users
   And could you please check my control files(in attachment)?
   I used Gromacs in this flow:
	1. Constructed my starting coordinates(conf.gro) by a piece of CPP code 
	2. ankyl.itp + C10.itp -> topol.top;
         3. Em.mdp is energy minimize control file;
	4. Main.mdp is md control file,

Thank you very much in advance!

Zhang Rayn

发件人: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org] 代
表 Anton Feenstra
发送时间: 2003年1月14日 16:41
收件人: gmx-users at gromacs.org
主题: Re: [gmx-users] about "LINCS WARNING"

>      I am trying to simulate the interface between alkyls & water, the 
> decane (C10 , declared in ffgmx.itp) and SOL (OPLS) are used.

First, you cannot mix force fields. If you use the ffgmx forcefield for 
your alkanes, you must use SPC (or SPCE) water, since that is what has been 
used when deriving the other ffgmx forcefield parameters. If you want to 
use OPLS water, you must also use OPLS parameters for your alkanes.

Second, if you want to minimize some more, you are better of using flexible 
waters. The constraints algorithms used for bond lengths and angles make it 
harder to minimize the energy. So, you should add that line define = 
-DFLEX_SPC back into your .mdp file.

Third, mdrun must optimize the step length for energy minimization, simply 
because when the step is too large, energy will go *up* in stead of down.

Fourth, I notice you use a 0.0001ps time step (i.e. 0.1 fs). As 
counterintuitive as that may seem, a very small step can also give rise to 
problems, which are related to the precision of the calculations. A step 
size below 1 fs should not be necessary for any normal mdrun.

Finally, I agree with Kun-Lin in that you probably have some problem in 
your initial conformation, e.g. overlap between atoms. I suggest you review 
the procedure by which you generate your starting coordinates. Ofcourse, if 
you explain to us what you did, we might help... ;-)


 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "I Used To Care, But Things Have Changed" (Bob Dylan)     |
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.

与联机的朋友进行交流,请使用 MSN Messenger: http://messenger.msn.com/cn 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: step.tar.gz
Type: application/x-gzip-compressed
Size: 6636 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20030121/348b5f01/attachment.bin>

More information about the gromacs.org_gmx-users mailing list