[gmx-users] Energy units

Hi all, This may be a silly and trivial question, but the energy unit given in Gromacs is kJ/mol. What I don't quite understand is, the energy is per mole of what exactly? The energy is system size dependent, so if I double the number of molecules, the energy will double accordingly. But

RE: [gmx-users] Energy units

for GROMACS users Subject: Re: [gmx-users] Energy units Cheong Wee Loong, Daniel wrote: Hi all, This may be a silly and trivial question, but the energy unit given in Gromacs is kJ/mol. What I don't quite understand is, the energy is per mole of what exactly? In a very real sense

[gmx-users] plain cutoff coulomb

Hi all, This seems like a really simple and silly question, but I have read through the manual and the archives and can't seem to find anything about it. If I were to set coulombtype = cutoff, g_energy will still calculate Coul-LR term which suggests that Gromacs calculates some long range

[gmx-users] charge distribution

Hi all, I am using g_potential to calculate the charge distribution of my system which consists of a protein layer covalently bound to some fatty acids. The protein layer by itself would have an overall negative charge but they system as a whole is neutral. My question is this: When I

RE: [gmx-users] mdp file for local pressure

Is there a local pressure version of Gromacs 4? I can only find Gromacs version 3.02 with local pressure. If there is, could you tell me where to get it? Thanks. Daniel From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf

RE: [gmx-users] Can we abstract any frame from the trajectory file(trr) and save it as a gro file?

You can use trjconv to extract a frame from the trajectory, e.g. trjconv �Cf xxx.trr �Co xxx.gro �Cb ttt �Ce ttt From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of wuxiao Sent: Wednesday, May 06, 2009 8:42 AM To:

RE: [gmx-users] g_sas

list for GROMACS users Subject: Re: [gmx-users] g_sas Cheong Wee Loong, Daniel wrote: Dear all, I am interested to calculate the hydrophobic and hydrophilic area of the surface of the protein layer I am simulating. It looked like g_sas would be able to give me what I was looking for. But I

RE: [gmx-users] g_sas

] On Behalf Of Justin A. Lemkul Sent: Friday, April 24, 2009 10:17 AM To: Gromacs Users' List Subject: Re: [gmx-users] g_sas Cheong Wee Loong, Daniel wrote: Thanks Justin for the reply. I did read the help and manual and understand that the output file can be the whole or part

RE: [gmx-users] g_sas

Ah ok. Fair enough. Thanks! -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Friday, April 24, 2009 10:48 AM To: Gromacs Users' List Subject: Re: [gmx-users] g_sas Cheong Wee Loong, Daniel wrote

RE: [gmx-users] g_sas

gives the buried surface area. So it makes sense calculating the area over Protein A, but it's just something different. Hope it's clear. Cheers, Tsjerk On Fri, Apr 24, 2009 at 4:48 AM, Justin A. Lemkul jalem...@vt.edu wrote: Cheong Wee Loong, Daniel wrote: Thanks for the explanation

RE: [gmx-users] localp

I think the local pressure can only be calculated with a modified unsupported version of gromacs that you can download. However, this was only done with gromacs version 3.0 not even 3.3 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On

[gmx-users] Differences in version 3.0 and 3.3

Hi Chris, Thanks for your reply. I pretty much only changed the executable. The top/itp files did have to be modified a little bit because the formats were different, but all the parameters were the same. I basically wrote a script to convert the formats. Besides all the other energy