Re: [gmx-users] choosing box vectors

2013-06-14 Thread gromacs query
Dear Justin, Thanks a lot. I used this and it works fine: editconf -f final.pdb -o final.gro -c -d 0.0 regards, Jiomm On Sat, Jun 15, 2013 at 3:09 AM, Justin Lemkul wrote: > > > On 6/14/13 8:08 PM, gromacs query wrote: > >> Dear Justin, >> >> I saw your tutorial ( >> http://www.bevanlab.bioc

Re: [gmx-users] choosing box vectors

2013-06-14 Thread Justin Lemkul
On 6/14/13 8:08 PM, gromacs query wrote: Dear Justin, I saw your tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html ) But my case is different. I can not even generate tpr file (trjconv as tutorial says) as it need box info Can

Re: [gmx-users] choosing box vectors

2013-06-14 Thread gromacs query
Dear Justin, I saw your tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html ) But my case is different. I can not even generate tpr file (trjconv as tutorial says) as it need box info Can you please suggest what can be the best possi

Re: [gmx-users] choosing box vectors

2013-06-14 Thread Justin Lemkul
On 6/14/13 7:37 PM, gromacs query wrote: Dear Justin, Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I dont want to use as I think they are wrong). In my case if I have already water molecules in my system then if I use: editconf -f del.pdb -o del.gro -c -d 0.0 -bt c

Re: [gmx-users] choosing box vectors

2013-06-14 Thread gromacs query
Dear Justin, Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I dont want to use as I think they are wrong). In my case if I have already water molecules in my system then if I use: editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic even now also I see pbc box (in vmd) it

Re: [gmx-users] choosing box vectors

2013-06-14 Thread Justin Lemkul
On 6/14/13 4:58 PM, gromacs query wrote: Dear All, I have two different membrane systems (membrane with waters only) already with me. So I dont need to add solvent molecules. So to start with simulation I need box size (last line in gro file). I used following command (for both cases): editc

[gmx-users] choosing box vectors

2013-06-14 Thread gromacs query
Dear All, I have two different membrane systems (membrane with waters only) already with me. So I dont need to add solvent molecules. So to start with simulation I need box size (last line in gro file). I used following command (for both cases): editconf -f del.pdb -o del.gro -c -bt cubic Firs