[gmx-users] Infinite polymer, pbc=full and LINCS

[Erik Lindahl]

Hi Malin,

 From my previous (pretty limited) experience with polymers I know  
that it is pretty common to run them without constraints, using 1 fs  
timesteps, and bond force constants that are significantly weaker  
than normal.

You can check the force field parameters used in the d.polych2  
benchmark from the Gromacs website.

Cheers,

Erik

On Nov 17, 2005, at 10:41 AM, Malin Bergenstråhle wrote:

> Hi,
>
> I am simulating a system of infinite polymer chains using pbc=full  
> and LINCS bond constraints.
> My system is unreliable and sometimes the simulations crash due to  
> LINCS complaining about too large bond rotations.
> I have now noted that it seems like LINCS gives warnings of the kind:
>
> Step 22525, time 67.575 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.000029 (between atoms 22 and 23) rms 0.000004
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     347    348   30.6    0.1000   0.1000      0.1000
>
> and the atoms are always situated on different sides of a periodic  
> bound. A question that now arises is whether this could be a bug  
> with pbc=full or whether there is a problem with my system. I am  
> using  Gromacs 3.3.
>
> Any suggestions about how I could check this or whatever about  
> whatever the problem could be I would be grateful.
>
> Best regards,
>
> Malin
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.

-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20051117/107c5e68/attachment.html>