[gmx-users] grompp with cg does have problem!

Erik Lindahl lindahl at sbc.su.se
Fri Dec 16 23:51:49 CET 2005


Mark is mostly right - the main reason is that we simply haven't  
found it worth the effort yet :-)

The underlying problem is that minimization is really sensitive to  
tiny differences in coordinates, and even conservative constraint  
algorithms usually leave constraint errors in the order of 1e-6. This  
can lead to really strange artifacts since your system is no longer  
strictly conservative, so if you want really good minimization the  
best bet is to allow the molecule to be flexible and use e.g. BFGS.

We're aware of it though, and will eventually add code to project out  
constraint forces with CG too, but for the above reason it's not a  
top priority!



On Dec 16, 2005, at 11:42 PM, Mark Abraham wrote:

> David Mobley wrote:
>> Mark,
>> It may well be the case that implicit water constraints are the  
>> problem, as the follow-up response seems to indicate (I haven't  
>> tried it myself). I guess I'd suggest that this be stated  
>> explicitly in the manual (and perhaps even in the section on input  
>> files which discusses options for minimizers, under the CG  
>> section, there should be a note saying that CG won't work with  
>> rigid water...).
> I filed a Bugzilla report for the same at http:// 
> bugzilla.gromacs.org/show_bug.cgi?id=37
>> Also, perhaps this is naive, but CG works fine in AMBER without  
>> doing anything special. It might be worth checking there to see  
>> how AMBER handles this. Perhaps it is "properly" handling the  
>> water, and if so, GROMACS could do the same thing? Or perhaps it  
>> lets the water be flexible? I'm not sure, but it seems like the  
>> issue must already be one people have dealt with in these other  
>> packages.
> It's probably just that constraints aren't implemented in the  
> gromacs CG algorithm. It's probably not worth implementing either,  
> given that constraints can be used with steepest descent and L-BFGS.
> Mark
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Erik Lindahl  <lindahl at sbc.su.se>     Backup address:  
<erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Stockholm Bioinformatics Center, Stockholm University, SE 106 91  
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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