Re: [gmx-users] Question regarding box size

Thanks Justin and Victor On Sat, Jul 11, 2015 at 9:12 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/15 1:35 AM, James Lord wrote: Hi all, I have a system with 300k atoms, but computationally it is expensive for me doing simulation with such a big system, Is it possible to reduce the

Re: [gmx-users] Question regarding box size

You can reduce the box size with editconf. If you start with a protein, you can add a layer of water of a given thickness by using genbox. Hope this helps Victor 2015-07-10 0:35 GMT-05:00 James Lord jjamesgreen...@gmail.com: Hi all, I have a system with 300k atoms, but computationally it is

Re: [gmx-users] Question regarding box size

On 7/10/15 1:35 AM, James Lord wrote: Hi all, I have a system with 300k atoms, but computationally it is expensive for me doing simulation with such a big system, Is it possible to reduce the box size? If yes how? (the .gro file is uploaded). I know from Justin tutorial genconf -nbox

[gmx-users] Question regarding box size

Hi all, I have a system with 300k atoms, but computationally it is expensive for me doing simulation with such a big system, Is it possible to reduce the box size? If yes how? (the .gro file is uploaded). I know from Justin tutorial genconf -nboxvector 1 1 1 Does the numbers after -nbox