[gmx-users] Unconstrained_start

[David]

On Mon, 2003-12-15 at 17:23, Hua Wong wrote:
> I have a question about the LINCS settings. I was obtaining a LINCS 
> warning each time I was launching mdrun for SA process. Only for the 
> firsts steps. Then the simulation continued...
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.000865 (between atoms 941 and 945) rms 0.000158
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     257    258   32.9    0.1090   0.1090      0.1090
> step 0
> Step 1, time 0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.000848 (between atoms 257 and 258) rms 0.000043
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     257    258   30.7    0.1090   0.1089      0.1090
> step 10, will finish at Fri Dec 12 12:36:40 2003
> step 20, will finish at Fri Dec 12 12:35:35 2003
> 
> Just like that.
> 
> So I tried modifying the parameters in the mdp file. 
> And at the line :
> unconstrained_start =
> I putted yes instead of no.

with yes the starting conformation is used as is, with no, before the
first step the constraints are applied. This is important for making
continuous continuation trajectories (then you want yes).
Usually you want no, to have your simulation start with correct bond
lengths, but this is not crucial if your starting coordinates are good.

> 
> Now it is working fine without warning 
> 
> 
> step 0
> step 10, will finish at Mon Dec 15 20:49:38 2003
> step 20, will finish at Mon Dec 15 20:37:43 2003
> step 30,
> 
> I just thought for a moment that it seemed logical; as it was always the 
> first steps that LINCS complained about.
>  
> But I am still wondering about the exact role of this setting. The start 
> configuration is : the .gro file I used as input for grompp? or the .gro 
> given by mdrun? 
> 
> What are the exact consequences of unconstrained start configuration? 
> (Have I found the right switch or will it be the source of further problems?) 
> 
> Thanks
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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