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

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 rela

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

Thank you for answer. I checked up my .gro and .top files, and even 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

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

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 : > Dear colleagues, > > I want to put in my cell a lot of molecules (f.e., 32 lipids), and I make for

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

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 s