Re: [gmx-users] problem vwith ethanol-water solution

2013-10-31 Thread Justin Lemkul
On 10/31/13 7:03 PM, Ehsan Sadeghi wrote: Thanks Justin, Here is the steps that I followed: pdb2gmx -f eth.pdb -o eth.gro -p eth.top pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5 genbox -cp box.gro -cs spc216.gro -c

Re: [gmx-users] problem vwith ethanol-water solution

2013-10-31 Thread Ehsan Sadeghi
From: "Justin Lemkul" To: "Discussion list for GROMACS users" Sent: Thursday, October 31, 2013 1:18:07 PM Subject: Re: [gmx-users] problem vwith ethanol-water solution On 10/31/13 2:25 PM, Ehsan Sadeghi wrote: > Hi gmx users, > > I want to solvate nafion molecules

Re: [gmx-users] problem vwith ethanol-water solution

2013-10-31 Thread Justin Lemkul
On 10/31/13 2:25 PM, Ehsan Sadeghi wrote: Hi gmx users, I want to solvate nafion molecules in a 3:1 ethanol water solution. I used genbox with -ci option to add ethanol to water when generating the box, but it did not work. Then, first I solvated the ethanol in water, and then added What "di

Re: [gmx-users] problem vwith ethanol-water solution

2013-10-31 Thread Riccardo Concu
Dear Ehsan, Did you try to pack your box with packmol? I have a similar system and packmol pack my system quite well and in a random way. Regards, Riccardo -Original Message- From: Ehsan Sadeghi Sent: Thursday, October 31, 2013 7:25 PM To: Discussion list for GROMACS users Subject: [g