[gmx-users] relative constraint deviation after lincs

[Justin A. Lemkul]

Alessandro Casoni wrote:
> hi users,
> I want to simulate a position restraint md.
> pdb2gmx creates a correct protein.top and  a posre.itp file.
> but when I use " define = -DPOSRES" I have this error:
> 
> Step 1004, time 2.008 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.026978, max 1.366297 (between atoms 646 and 647)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>    646    647   90.0    0.2562   0.2366      0.1000
> 
> and the simulation gives me a fatal error...
> 
> in my gro file atom 646 and 647 are:
> 65ASN      N  646   8.608   5.187   2.517
> 65ASN      H  647   8.510   5.206   2.518
> 
> please, give me some tips...
> 

This has to be the most frequently-reported problem.  Therefore, there are 
thousands of posts in the list archive that may help.  Also, from the wiki:

http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

-Justin

> Alessandro
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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