Re: [gmx-users] Gromacs inquiries

2011-10-26 Thread Mark Abraham
On 26/10/2011 5:18 PM, cuong nguyen wrote: Dear Mark, I used to put ten molecules of hexanol in a box 5 5 1 with the instruction "genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p hexanol.top". However, now I want to fill up the box 4 4 4 with hexanol molecules. If I change the numbe

Re: [gmx-users] Gromacs inquiries

2011-10-26 Thread Justin A. Lemkul
cuong nguyen wrote: Dear Mark, I used to put ten molecules of hexanol in a box 5 5 1 with the instruction "genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p hexanol.top". However, now I want to fill up the box 4 4 4 with hexanol molecules. If I change the number 10 in the instructi

Re: [gmx-users] Gromacs inquiries

2011-10-25 Thread cuong nguyen
Dear Mark, I used to put ten molecules of hexanol in a box 5 5 1 with the instruction "genbox -ci hexanol.gro -nmol 10 -box 5 5 1 -o layer.gro -p hexanol.top". However, now I want to fill up the box 4 4 4 with hexanol molecules. If I change the number 10 in the instruction to 1000 or 1, it wil

Re: [gmx-users] Gromacs inquiries

2011-10-25 Thread Mark Abraham
On 26/10/2011 1:46 PM, cuong nguyen wrote: Dear, Thanks a lot for useful software. I am trying to generate a box (4 4 4) with full hexanol molecules inside. I have used the instruction "genbox -ci hexanol.GRO -box 4 4 4 -o layer.gro -p hexanol.top", however it has not been successful. Unfor