[gmx-users] problem with gromacs

Hello Folder with the program GROMACS save in a folder cygwin / home / Sylwia. then: $ cd gromacs-4.5.5 ./configure --enable-sse --enable-float no errors occurred only at the end: configure: WARNING: unrecognized options: - enable-sse make no errors occurred only at the end:

Re: [gmx-users] problem with gromacs

On 9/01/2012 3:44 AM, Sylwia Chmielewska wrote: Hello Folder with the program GROMACS save in a folder cygwin / home / Sylwia. then: $ cd gromacs-4.5.5 ./configure --enable-sse --enable-float no errors occurred only at the end: configure: WARNING: unrecognized options: - enable-sse You'll

Re: [gmx-users] free energy (coordinates file)

On 7/01/2012 9:12 PM, parto haghighi wrote: Dear GMX users, I have a question about 6th gromacs tutorial. That's not a useful description, because nobody else knows what list you're looking at. A URL is much better. I have to perform 5 steps of calculation contain: 1) EM-1 2) EM-2 3) NVT

[gmx-users] Nematic Order Parameter of Organic Liquid Crystals

Hi, I would like to calculate the nematic order parameter of organic liquid crystals. Is it possible to use the 'g_order' command in gromacs to do that? Or do I need to write my own script? Or are there softwares/scripts out there that can already do the job? Thanks, Serene This email and

[gmx-users] regarding nvt

hello sir, Thanks for your reply. Intensionally i didnt neutralise my system.. i am using version 3.3.3.. i like to know is there anything wrong in using maxwarn in my commamd? did maxwarn ll affect my result sir ? Thanking you, -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] regarding nvt

On 9/01/2012 3:08 PM, priya thiyagarajan wrote: hello sir, Thanks for your reply. Intensionally i didnt neutralise my system.. Well you're probably not modelling reality. i am using version 3.3.3.. You'll get much better performance and useful help if you update. i like to know is

[gmx-users] Superimposing dissimilar structures

Hello everyone, I've used the rot+trans option in GROMACS trjconv to superimpose groups of atoms within a single molecular dynamics simulation.  I am now interested in modeling a protein, and a rather thoroughly scrambled circular permutation of that same protein.  I want to construct a

Re: [gmx-users] Superimposing dissimilar structures

On 9/01/2012 4:53 PM, John Ladasky wrote: Hello everyone, I've used the rot+trans option in GROMACS trjconv to superimpose groups of atoms within a single molecular dynamics simulation. I am now interested in modeling a protein, and a rather thoroughly scrambled circular permutation of that

[gmx-users] Hello

Hello, I am working on Heme containing proteins, is it necessary to treat Heme group as Ligand. Best nirmal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

Re: [gmx-users] Hello

On 9/01/2012 6:42 PM, Nirmal Prasad wrote: Hello, I am working on Heme containing proteins, is it necessary to treat Heme group as Ligand. What do you mean by treating as a ligand? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Regarding AIB RESIDUE NOT FOUND IN RESIDUE TOPOLOGY DATABASE

Hello sir, I am using gromacs 4.5.3 version. I am doing 12 amino acid peptide simulation. But my peptide have some non standard amino acid like AIB,NLE After fire pdb2gmx comand i am getting follwing error in simulation. ''Residue NLE not found in residue topology database.'' What to do next

Re: [gmx-users] Hello

Dear Mark, Thanks for responding. I am new to Gromacs. I am working on Cytochrome P 450 proteins, these proteins contain HEME group. For MD run should I prepare separate protein and HEME group topologies and reconstruct protein-HEME complex. Is this procedure is correct or not. nirmal On