Re: [gmx-users] EDLC simulation using Gromacs

2014-06-29 Thread Dr. Vitaly Chaban
It is very easy. You apply an electric field and observe how DL is forming. Have fun. Dr. Vitaly V. Chaban On Fri, Jun 27, 2014 at 3:14 PM, Andy Chao ac...@energiaq.com wrote: Dear Users, Would you please suggest a few examples of using GROMACS to simulate an EDLC device? Thanks a lot!

[gmx-users] How to calculate Box Vectors in the last line of the .gro file?

2014-06-29 Thread Todor Antonijevic
Hi, I cannot obtain the last line (box vectors *1.82060 1.82060 1.82060*) of the .gro file. *Can anyone explain me how the last line is calculated?* The example is from the manual: MD of 2 waters, t= 0.0 6 1WATER OW11 0.126 1.624 1.679 0.1227 -0.0580 0.0434 1WATER

Re: [gmx-users] How to calculate Box Vectors in the last line of the .gro file?

2014-06-29 Thread Justin Lemkul
On 6/29/14, 3:06 PM, Todor Antonijevic wrote: Hi, I cannot obtain the last line (box vectors *1.82060 1.82060 1.82060*) of the .gro file. *Can anyone explain me how the last line is calculated?* The example is from the manual: MD of 2 waters, t= 0.0 6 1WATER OW11 0.126

[gmx-users] GROMACS 5.0 official release

2014-06-29 Thread Mark Abraham
Hi GROMACS users, The official release of GROMACS 5.0 is available! What new things can you expect? * GROMACS now uses a combination of *C++98* and C99, so you will need a working C++ compiler that is intended to work with your C compiler * Building GROMACS now requires *CMake version 2.8.8*,

[gmx-users] Questions regarding converting .GRO files to .TOP files

2014-06-29 Thread Andy Chao
Dear GROMACS users: I have a few questions about converting the .GRO files to .TOP files. I first used Python to create a sheet of graphene layer by using the following Python codes: from ase import * from ase.structure import graphene_nanoribbon from ase io.import* gnr1 =