[gmx-users] Re: generating user-defined topologies for surfaces

2013-07-31 Thread Valentina
perfect! -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010235.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

Re: [gmx-users] Re: generating user-defined topologies for surfaces

2013-07-31 Thread Justin Lemkul
On 7/31/13 8:57 AM, Valentina wrote: Sorry, still confused here: I have a cell, that is same as residue, contains an inorganic crystal. But since I am creating a surface I have bonds going across periodic boundary, like Al and O shown on the pic? Can I still do it? How do I input it into molec

[gmx-users] Re: generating user-defined topologies for surfaces

2013-07-31 Thread Valentina
Sorry, still confused here: I have a cell, that is same as residue, contains an inorganic crystal. But since I am creating a surface I have bonds going across periodic boundary, like Al and O shown on the pic? Can I still do it? How do I input it into molecule.rtp? Thank you, V

[gmx-users] Re: generating user-defined topologies for surfaces

2013-07-30 Thread Valentina
Thank you. So it is only involved in pdb2gmx, but not in the simulation itself - perfect. For some reason I assumed it is checked through the simulation. Writing it now. -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192

Re: [gmx-users] Re: generating user-defined topologies for surfaces

2013-07-30 Thread Justin Lemkul
On 7/30/13 9:58 AM, Valentina wrote: A follow up question - does searching for neighbouring atoms to bond to according to specbond.dat slow down calculation and if so how significantly. I've never seen specbond.dat affect pdb2gmx by more than a few seconds, but it depends on the size of th

[gmx-users] Re: generating user-defined topologies for surfaces

2013-07-30 Thread Valentina
A follow up question - does searching for neighbouring atoms to bond to according to specbond.dat slow down calculation and if so how significantly. Thanks! -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010196.ht

[gmx-users] Re: generating user-defined topologies for surfaces

2013-07-30 Thread Valentina
Great, thank you, Justin. -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010195.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://li