[gmx-users] P-coupling in vacuum, inflexibility

[Pavel Semenyuk]

Thank you for answer.
I checked up my .gro and .top files, and even if I make it from pdb using pdb2gmx,
simulation crashes. But without constraints or with all-bonds constraint, it work
finely. But all-angles constraint results warnings (no p-coupling):
--
Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 21018.706436, max 77109.148438 (between atoms 1161 and 1162)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      1      2   31.6    4.4548 104.4365      0.2401
   1595   1597  177.4    0.3032   0.1406      0.2522
   1594   1596  169.8    0.2330   0.4373      0.2522
--
How can I fix it?
Thank you..

Best regards,
Pavel I. Semenyuk

On Wed, 6 May 2009 21:44:00 +0200, Tsjerk Wassenaar wrote
> Hi Pavel,
> 
> It seems that your molecules are broken over the periodic boundaries.
> Make sure that you set up your coordinates and topology file
> correctly.
> 
> Cheers,
> 
> Tsjerk
> 
> 2009/5/6 Pavel Semenyuk <psemenyuk at belozersky.msu.ru>:
> > Dear colleagues,
> >
> > I want to put in my cell a lot of molecules (f.e., 32 lipids), and I make for it a very
> > big box, put my molecules into this box (without water) and then do simulations with
> > pressure coupling to make my box smaller. So, how can I make my molecules inflexible? if
> > I set links or shake constraints, it results too many warnings ("Warning: 1-4
> > interaction between 12 and 33 at distance 30.841 which is larger than the 1-4 table size
> > 2.400 nm").
> > Thank you...
> >
> > Best regards,
> > Pavel I. Semenyuk
> >
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> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
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> The Netherlands
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