Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140

Add the following line to your .bashrc or .cshrc source /usr/local/gromacs/bin/GMXRC and then everytime you open a new terminal gromacs will be auto sourced. Regards, Sarath -- Sarath Chandra Dantu, PhD, ELS Room No. 606, New BSBE Building Department of Biosciences and Bioengineering Indian

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140

Sorry, I found my error, should have used DGMX .. However, another problem arose after installation. The program ran fine in that terminal by which I installed gromacs, but when I closed that terminal and opened another terminal, after typing gmx -h , it showed The program 'gmx' is currently

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140

While rebuilding ,I gave the command cmake .. -GMX_USE_RDTSCP=OFF But, it showed the error CMake Error: Could not create named generator MX_USE_RDTSCP=OFF Am I making any errors ? On Mon, Apr 25, 2016 at 12:18 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send

[gmx-users] Standard volume of the simulation box

hi how can i find the standard volume of the simulation box, that includes ligand, protein and water. Sana Saeed Khan, Research Assistant Chemoinformatics Lab Graduate Student, MS bioinfo Department of Bioinformatics Soongsil University, Seoul, South Korea. -- Gromacs Users mailing list *

[gmx-users] g_helix

Dear all, I have a question regarding to calculate g_helix, I am not sure about the index numbers for using g_helix! Should I use the all atom numbers of protein that I have? If not please explain to me which indexes of protein I have to choose. The same for do_dssp, I have to use the all atom

[gmx-users] how to convert CHARMM36 system into virtual site system?

Hello: I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just wondering how can we convert the lipids molecule to virtual site lipids? Thank you very much Albert -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

Hi, Thanks a lot ! I'll try it,.. Regards, Husen On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul wrote: > > > On 4/24/16 12:04 AM, Husen R wrote: > >> Dear all, >> >> is there any complete documentation discussing checkpoint/restart in >> Gromacs-5.1.2 ? >> I found this link

Re: [gmx-users] Graphene sheet topology

Thanks Justin as always for your prompt reply. I have now created the graphene topology the way u suggested that is I issued the following command 1. g_x2top -f file.gro -o graphene.top -pbc: I did not prefer to use the -noparam option since it does not print the k0, k1 and similar values. 2. I

Re: [gmx-users] Error in mdrun

On 4/24/16 8:06 AM, Roshan Shrestha wrote: How to turn off that option ? I mean, the error cam up when I typed gmx mdrun -deffnm em -v So, what should command I use to turn off that option. Thanks "Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option." You have to re-compile

Re: [gmx-users] Error in mdrun

How to turn off that option ? I mean, the error cam up when I typed gmx mdrun -deffnm em -v So, what should command I use to turn off that option. Thanks On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha wrote: > My CPU configuration is rather too old, > Architecture:

Re: [gmx-users] Graphene sheet topology

On 4/23/16 1:37 AM, soumadwip ghosh wrote: Hello all, I am currently working on the interaction between a flat graphene sheet and nucleic acids at various physiological conditions. I am using CHARMM 27 force field and GROMACS 4.5.6 for MD simulations. Here is my work order 1. I

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

On 4/24/16 12:04 AM, Husen R wrote: Dear all, is there any complete documentation discussing checkpoint/restart in Gromacs-5.1.2 ? I found this link that discuss checkpoint ( http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and this link that discuss restart (

[gmx-users] md example for protein complex dissociation

Dear All, Will you please show me examples that with by biological significance, a protein complex dissociated into its sub-unit during the md process? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Error in mdrun

Hi, You could try rebuilding with that option turned off :-) Mark On Sun, Apr 24, 2016 at 1:15 PM Roshan Shrestha wrote: > My CPU configuration is rather too old, > Architecture: i686 > CPU op-mode(s):32-bit, 64-bit > Byte Order:Little Endian

[gmx-users] Error in mdrun

My CPU configuration is rather too old, Architecture: i686 CPU op-mode(s):32-bit, 64-bit Byte Order:Little Endian CPU(s):2 On-line CPU(s) list: 0,1 Thread(s) per core:1 Core(s) per socket:2 Socket(s): 1 Vendor ID: