[gmx-users] P-coupling in vacuum, inflexibility
psemenyuk at belozersky.msu.ru
Thu May 7 22:22:45 CEST 2009
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?
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
> 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
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