Re: [gmx-users] Re: general question about molecule.rtp and pdb2gmx

2013-08-27 Thread Justin Lemkul
On 8/27/13 4:25 PM, Valentina wrote: Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent this output. No, that's not how gen-pairs works. There are many excellent explanations of how it works in the list archive, but suffice it to say it does not affect the appearan

[gmx-users] Re: general question about molecule.rtp and pdb2gmx

2013-08-27 Thread Valentina
Yes - own parameters. Just thought gen-pairs in [ defaults ] should prevent this output. Thank you -- View this message in context: http://gromacs.5086.x6.nabble.com/general-question-about-molecule-rtp-and-pdb2gmx-tp5010759p5010764.html Sent from the GROMACS Users Forum mailing list archive at

Re: [gmx-users] Re: general question about molecule.rtp and pdb2gmx

2013-08-27 Thread Sergey
Yes, can remove. However, ability to remove don't depend on our desire, but depend on Force field set of rules. If molecule was parametrized with 1-4 LJ, it is not desirable to remove it. If it is in-house force field which ignore 1-4 LJ, then one can safely remove it. Sergey 27.08.2013, 20:42

[gmx-users] Re: general question about molecule.rtp and pdb2gmx

2013-08-27 Thread Valentina
Ok, thank you! I was hoping for an easier job. My system is anyhow flying apart - trying to spot a problem. Hence trying. One more question - [ pairs ] get automatically generated. But I don't need 1-4 LJ. So I can just remove them? Thank you -- View this message in context: http://gromacs.