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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 6 21:44:00 CEST 2009

Hi Pavel,

It seems that your molecules are broken over the periodic boundaries.
Make sure that you set up your coordinates and topology file



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
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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