[gmx-users] RE: tutorials for Coarse-Grained MD Simulation

Dear Jan, Thanks for the link. The tutorials available here are very helpful start preparing the systems for simulation but would like to know how to merge the custom version of Gromacs for CG available in Martini web site with my existing Gromacs installation. Moreover how to make use of all the

Re: [gmx-users] NMA and g_nmeig segmentation fault

On 7/08/2012 7:07 AM, Michael Howard wrote: Hello All -- I'm trying to do a normal modes analysis of a fairly large crystal system (~20,000 atoms) in double-precision GROMACS. The system is xy periodic with 2 9-3 walls, and has periodic molecules. I first minimized the structure with L-BFGS to 1e

[gmx-users] NMA and g_nmeig segmentation fault

Hello All -- I'm trying to do a normal modes analysis of a fairly large crystal system (~20,000 atoms) in double-precision GROMACS. The system is xy periodic with 2 9-3 walls, and has periodic molecules. I first minimized the structure with L-BFGS to 1e-5 tolerance with switched vdW interactions an

Re: [gmx-users] Hydroxyapatite MD odd behavior

On 8/6/12 3:13 PM, Ramon Garduno wrote: On Mon, 06 Aug 2012 13:52:46 -0400, Justin Lemkul wrote Please provide all the necessary files, including topologies and modified force field files. I don't have time to make and double- check all of these files and it's better to use exactly the same

Re: [gmx-users] Hydroxyapatite MD odd behavior

On Mon, 06 Aug 2012 13:52:46 -0400, Justin Lemkul wrote > Please provide all the necessary files, including topologies and > modified force field files. I don't have time to make and double- > check all of these files and it's better to use exactly the same > files you've been trying to use. >

Re: [gmx-users] Hydroxyapatite MD odd behavior

On 8/6/12 1:35 PM, Ramon Garduno wrote: Justin, Of course you are right, for troubleshooting the smaller, the better. However, in order to build a hydroxyapaptite (HAP) slab we need the proper unit cell, the later is by no means small. In response to your comments, I will appreciate very much

[gmx-users] Re: How to add new residue(LIG reisdue)? (Justin Lemkul)

Please keep all Gromacs-related correspondence on the gmx-users mailing list. On 8/6/12 1:47 PM, Ali Alizadeh wrote: Dear Justin I Know your reply. But, All my pdb file for each molecules contain LIG residue. What's LIG residue? Why LIG residue exists in any pdb files, I used avogadro softwar

Re: [gmx-users] Hydroxyapatite MD odd behavior

Justin, Of course you are right, for troubleshooting the smaller, the better. However, in order to build a hydroxyapaptite (HAP) slab we need the proper unit cell, the later is by no means small. In response to your comments, I will appreciate very much if you could examine the PDB files related

[gmx-users] Compilation of Gromacs 4.5.5 with GPU support: libxml and CUDA toolkit problems

Hi, I am trying to compile Gromacs 4.5.5 with GPU support on Linux. I have performed the following steps: export OPENMM_ROOT_DIR=/home//gromacs/OpenMM2.0-Linux64/ mkdir build-gpu mkdir exec-gpu cd build-gpu cmake ../ -DGMX_OPENMM=ON -DFFTW3F_INCLUDE_DIR=/usr/lib/include -DFFTW3F_LIBRARIE

Re: [gmx-users] a residue move in extremely large scale in MD

On 6/08/2012 8:58 PM, Acoot Brett wrote: Dear All, I have a protein with about 400 amino acids. I have done a production MD of it. I find in the 400 amino acids, there is 1 amino acids, during the whole MD process, this residue moves in a extremely large scope in comparison with all the oth

[gmx-users] a residue move in extremely large scale in MD

 Dear All, I have a protein with about 400 amino acids. I have done a production MD of it. I find in the 400 amino acids, there is 1 amino acids, during the whole MD process, this residue moves in a extremely large scope in comparison with all the other residues. Do you think this single residu

Re: [gmx-users] Re: Adding New Residue to the Gromos 53.6 ff

On 6/08/2012 6:00 PM, James Starlight wrote: Mark, The main difficulties is that ATB's output is in the form like [ bonds ] 122 0.1000 1.8700e+07 132 0.1000 1.8700e+07 [ angles ] ; ai aj ak funct angle fc 2132109.50 380.

Re: [gmx-users] Re: Adding New Residue to the Gromos 53.6 ff

Mark, The main difficulties is that ATB's output is in the form like [ bonds ] 122 0.1000 1.8700e+07 132 0.1000 1.8700e+07 [ angles ] ; ai aj ak funct angle fc 2132109.50 380.00 2142109.50 425.00 3

Re: [gmx-users] Create a elastic network model -attach a spring between to atoms with force constant

On 6/08/2012 5:24 PM, mohan maruthi sena wrote: Hi all, I want to create an elastic network model for a protein, in which i have selected only c-alpha atoms(removed rest of the atoms). To attach a spring between alpha atoms with some force(spring) constant k , How can i mention

RE: [gmx-users] tutorials for Coarse-Grained MD Simulation

For MARTINI force field: http://md.chem.rug.nl/cgmartini/index.php/tutorial Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of J Peterson [think_bey...@aol.com] Sent: Monday, August 06, 2012 6:41 AM To: gmx-users@gromacs

[gmx-users] Create a elastic network model -attach a spring between to atoms with force constant

Hi all, I want to create an elastic network model for a protein, in which i have selected only c-alpha atoms(removed rest of the atoms). To attach a spring between alpha atoms with some force(spring) constant k , How can i mention this in topology file ? Thanks, Mohan -- gmx-u