[gmx-users] Re: [gmx-developers] More than one settle type

[Justin A. Lemkul]

I am CC'ing this message to the gmx-users list; please continue any future 
discussion there.  I hadn't realized it was initially posted to gmx-developers, 
which is the wrong forum for such questions.  Comments inline below.

Emanuel Birru wrote:
> Hi Jestin,
> 
> Thanks for your advise. Just to make sure that whether I understand you
> well or not, 
> 
> Are you suggesting me to put additional constraints on the topology as
> below
> [ settles ]
> ; OW    funct   doh     dhh
> 1       1       0.1     0.16330
> 1       1       0.1     0.16330
> 1       1       0.1     0.16330
> 
> Which supposed to represent O-H and H-H in addition to the original O-W?
> 

Yes, but what you've posted is wrong.  You need a [constraints] directive that 
does indeed replace the effect of [settles].  What you've posted above does not 
accomplish that goal and will result in the same fatal error.

-Justin

> Thanks,
> Emanuel 
> 
> 
> -----Original Message-----
> From: gmx-developers-bounces at gromacs.org
> [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of Justin A.
> Lemkul
> Sent: Friday, 15 October 2010 12:11 PM
> To: Discussion list for GROMACS development
> Subject: Re: [gmx-developers] More than one settle type
> 
> 
> 
> Emanuel Birru wrote:
>> Hi,
>>
>>  
>>
>> I am about to calculate partition coefficient of a water molecule
> using 
>> gromacs 4.0.7 . To do the calculation I used spc water model as a 
>> solvent and as a solute, I just changed the solute's residue name and 
>> use the same itp file as the spc.itp of gromacs with the name sol.itp.
> I 
>> can manage to put them in a box as a solute and solvent, but the
> problem 
>> arise when I start doing minimization. I tried to minimised using
> L-BFGS 
>> and steep. The error message that I got is the following
>>
>> "Fatal error:
>>
>> More than one settle type.
>>
>> Suggestion: change the least use settle constraints into 3 normal 
>> constraints."
>>
>>  
>>
>> You can get the minimization mdp (em1 and em2) files and my solute itp
> 
>> file (sol) at the following link.
>>
>> http://hydra.pharm.monash.edu.au/md_project/em1.txt
>>
>> http://hydra.pharm.monash.edu.au/md_project/em2.txt
>>
>> http://hydra.pharm.monash.edu.au/md_project/sol.txt
>>
>>  
>>
>> Could any one suggest a solution please.
>>
> 
> There are solutions in the list archive and in the error message itself.
> You 
> cannot have two separate blocks of molecules (water) that use SETTLE.
> Use an 
> equivalent [constraints] directive to mimic the effects of SETTLE,
> defining two 
> O-H constraints and an H-H constraint.
> 
> -Justin
> 
>>  
>>
>> Cheers,
>>
>> Emanuel
>>
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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