Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

Hi Nidhin, Insane allows you to build lipids from the command line. Alternatively, it's pretty easy to add DOTAP to insane, using the templates inside. If you feel you need a hand with that, let me know. Cheers, Tsjerk On Jun 7, 2016 12:21 AM, "Nidhin Thomas"

[gmx-users] How to fix the ends of the protein?

Dear Gromacs users, I would like to simulate the topological domain of one protein. For that I need to fix the ends of the simulated protein. How do one can fix(constraint) the ends of the protein? Kindly help me how to do this fixation? Surya Graduate student India. -- Gromacs Users mailing

[gmx-users] cannot output all the structures of one cluster

Dear GMX users, I want to output all the structures of certain cluster using g_cluster, and the following is my command: g_cluster -f md5_mol.xtc -s md5.tpr -n index.ndx -o md5.xpm -g md5_cluster.log -cutoff 0.12 -cl cluster1.gro -wcl 1 -nst 30 While it seems gromacs cannot generate all the

Re: [gmx-users] Non-bonded energy

Hi, So, for calculating non-bonded energy, we have to consider all pair of atoms of the protein which are separated by a distance less than the cutoff distance. Please correct me if I am wrong. - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent:

Re: [gmx-users] Position restrain of of different chain in fibril structure

Dear all good day. https://drive.google.com/open?id=0B9FUC_dv9IRoTUdHZENEN1FaOHc In the google drive file i attached all the file with forcefield file. I only deleted the nvt.trr file. As this file size very big. In this run i only use 7 chain of cellulose. to small the calculation step. Still

[gmx-users] Position restrain of of different chain in fibril structure

Dear all I have a structure file of cellulose nano fibril of 36 chain (each have 40 residue). I want to simulate it as a single compound. I try to run the simulation with OPLS-AA force field. After energy minimization when i run the equilibrium step then the fibril structure broken and all the

Re: [gmx-users] Non-bonded energy

On 6/6/16 9:00 AM, ABANTIKA PAL wrote: Hi, I want to know which atoms are to be considered while calculating non-bonded energy of a protein. Whether it is all pair atom or there is a particular criteria while selecting the atoms. The nonbonded energy of a protein would imply that any

Re: [gmx-users] Position restrain of of different chain in fibril structure

On 6/6/16 9:13 PM, Md. Imrul Reza Shishir wrote: Dear all I have a structure file of cellulose nano fibril of 36 chain (each have 40 residue). I want to simulate it as a single compound. I try to run the simulation with OPLS-AA force field. After energy minimization when i run the equilibrium

[gmx-users] Non-bonded energy

Hi, I want to know which atoms are to be considered while calculating non-bonded energy of a protein. Whether it is all pair atom or there is a particular criteria while selecting the atoms. Thanks. Abantika -- Gromacs Users mailing list * Please search the archive at

[gmx-users] gmx gangle selections help

Hello gromacs users, I want to map the angle between a specific bond vector (defined by the atoms A and B) and the z axis using gmx gangle. I am only interested in bond vectors that have a center-of-mass z-coordinate greater than C. Is there a way to make this selection using the 'gmx

[gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

Hi GROMACS Users, I would like to create a mixed bilayer of DPPC and DOTAP lipids for research. I usually use charm-gui or insane.py to create a mixed bilayer. But I could not find DOTAP listed in either of these lists. When I searched online, I got a mixed bilayer system for DMPC & DPPC lipids