[gmx-users] Unconstrained_start

[Hua Wong]

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.

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

-- 
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| Wong Hua (Student)                                       |
| Equipe de Bioinformatique Genomique et Moleculaire       |
| INSERM U436 Universite ParisVII     _____________________|
| 2 place Jussieu case 7113          | Tel:None            |
| 75251 PARIS Cedex 05               | Fax:None            |
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