[gmx-users] Building gromacs on CRAY XC40

Dear Gromacs users, I am trying to build gromacs on our latest supercomputer CRAY XC40, but the following errors using gcc and fftw. Here's my list of module loaded and install script, can anyone give any instructions? =

[gmx-users] Hexagonal prisms box

Hello, I'm trying to simulate a membrane in a hexagonal prism (I set it up with INSANE Python script for Martini, as I believe is actually the option by default) but when I visualize it in VMD it shows as triclinic. I attempted a solution I found on another discussion: trjconv -f

[gmx-users] installing GROMACS

Hi; I tried to install GROMACS using "Installation guide for GROMACS 5.0.5" in the gromacs.org, but I got an error after typing "cmake .. " line, then I tried "sudo apt-get install gromacs" command, it installed the gromacs-4.6.5 but I want the gromacs-5.0.5. what should I do? Thank you,

[gmx-users] Fw: JUSTIN kalp in dppc tutorial

- Forwarded Message - From: ‪neda razavi‬ ‪ To: "gromacs.org_gmx-users-requ...@maillist.sys.kth.se" Sent: Sunday, 4 October 2015, 13:07:50 Subject: JUSTIN kalp in dppc tutorial Why did

[gmx-users] Fw: problem with Justine tutorial

- Forwarded Message - From: ‪neda razavi‬ ‪ To: "gromacs.org_gmx-users-requ...@maillist.sys.kth.se" Sent: Sunday, 4 October 2015, 13:02:19 Subject: problem with Justine tutorial What does "add

[gmx-users] Fw: InflateGRO script in KALP in DPPC tutorial

Hello every body I read in InflateGRO file that : [ A distance cutoff in A can be defined : only lipids with a P-cA distance exceeding that cutoff will be written. ]  i want to know WHY and P-CA distance is from one lipid or two lipids??and P refers to p-atom or protein molecule??what is

[gmx-users] Fw: InflateGRO script in KALP in DPPC tutorial

- Forwarded Message - From: ‪neda razavi‬ ‪ To: "gromacs.org_gmx-users-requ...@maillist.sys.kth.se" Sent: Sunday, 4 October 2015, 21:25:30 Subject: InflateGRO script in KALP in DPPC tutorial Hello

[gmx-users] question about InflateGRO

Hello every body I read in InflateGRO file that : A distance cutoff in A can be defined : only lipids with a P-alpha carbon distance exceeding that cutoff will be written. i want to know WHY?and P-C alpha distance is from one lipid or two lipids??and P refers to p-atom or protein molecule??what

Re: [gmx-users] Fw: JUSTIN kalp in dppc tutorial

On 10/4/15 1:25 PM, ‪neda razavi‬ ‪ wrote: - Forwarded Message - From: ‪neda razavi‬ ‪ To: "gromacs.org_gmx-users-requ...@maillist.sys.kth.se" Sent: Sunday, 4 October 2015, 13:07:50 Subject:

Re: [gmx-users] Fw: InflateGRO script in KALP in DPPC tutorial

On 10/4/15 2:02 PM, ‪neda razavi‬ ‪ wrote: Hello every body I read in InflateGRO file that : [ A distance cutoff in A can be defined : only lipids with a P-cA distance exceeding that cutoff will be written. ] i want to know WHY and P-CA distance is from one lipid or two lipids??and P

Re: [gmx-users] question

On 10/4/15 1:57 PM, Andrew Bostick wrote: Dear Justin, My previous problem was solved after I used all-bonds instead of hbonds in constraint section of mdp file. (I got the topology for my ligand using antechamber). After completion of NVT equilibration phase, I viewed nvt.gro using vmd.

Re: [gmx-users] Fw: problem with Justine tutorial

On 10/4/15 1:27 PM, ‪neda razavi‬ ‪ wrote: - Forwarded Message - From: ‪neda razavi‬ ‪ To: "gromacs.org_gmx-users-requ...@maillist.sys.kth.se" Sent: Sunday, 4 October 2015, 13:02:19 Subject:

[gmx-users] question

Dear Justin, My previous problem was solved after I used all-bonds instead of hbonds in constraint section of mdp file. (I got the topology for my ligand using antechamber). After completion of NVT equilibration phase, I viewed nvt.gro using vmd. Please see the related figure in the following

Re: [gmx-users] h-bonds by g_hbond and VMD and ptraj

Hi Ondrej, They use different angles to determine if it is a bond or not. See respective manuals. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

Hi, Sorry for the delay in reply. I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1 version. My Desktop is 32-bit whereas my xtc files were generated on our super cluster, which runs on 64-bit O.S. On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola wrote: >