[gmx-users] Simulation of pure water

Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I

Re: [gmx-users] RMSD analysis

Dear Justin I think I have confused so much. Let me try to put it in simple way. 1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of monomer(just protein) to explain stability? 2. Time step of monomer(just protein) simulation is 150ns and protein-ligand complex is 50ns. In

Re: [gmx-users] RMSD analysis

On 6/6/17 1:11 PM, RAHUL SURESH wrote: Dear Justin Thank you. I am considering Rmsd rmsf rg as just supplementary analysis for my study. My aim to analyse conformational change in protein. I would like to bring a note on protein stability after ligand binding. I don't know to which part of

Re: [gmx-users] Usage of position restraint during FEP calculation

On 6/6/17 3:45 PM, Геннадий Макаров wrote: Dear GROMACS users, I want to estimate binding free energy for small ligand using procedure from article doi:10.1021/jp0217839 that imlies application of one distance, two angle and three dihedral restraints to ligand relatively to receptor. These

Re: [gmx-users] metal ions in equilibration step

On 6/6/17 8:22 AM, Mahboobeh Eslami wrote: Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are two calcium ions in the protein structure. These ions play an important role. In the equilibration step, should I consider protein,ligand and calcium ions as one

[gmx-users] Usage of position restraint during FEP calculation

Dear GROMACS users, I want to estimate binding free energy for small ligand using procedure from article doi:10.1021/jp0217839 that imlies application of one distance, two angle and three dihedral restraints to ligand relatively to receptor. These restraints are controlled by option 

[gmx-users] Energy Minimisation

Hi all, I have used the steepest descent method to minimise my system. It kept saying certain water molecules could not be settled but it still managed to reached the maximum force. Then I used the Conjugate gradient method and I get this error message. Can someday please tell me how I would

[gmx-users] Fw: mdp options in GROMACS 4.5.5

Hi João, Thank you very much. I removed this line from the mdp file. Regards,Mohammad From: João Henriques To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com Sent: Tuesday, 6 June 2017, 20:18:51 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5

Re: [gmx-users] RMSD analysis

Dear Justin Thank you. I am considering Rmsd rmsf rg as just supplementary analysis for my study. My aim to analyse conformational change in protein. I would like to bring a note on protein stability after ligand binding. I don't know to which part of monomer I can compare the rmsd of complex

Re: [gmx-users] mdp options in GROMACS 4.5.5

Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, not the integration). /J On Tue, Jun 6, 2017 at 5:45 PM, João Henriques wrote: > Hi! > > I'm not sure Verlet was already implemented in GMX 4.5.5, but check the > manual for that

Re: [gmx-users] mdp options in GROMACS 4.5.5

Hi! I'm not sure Verlet was already implemented in GMX 4.5.5, but check the manual for that version (or the closest one). Cheers, /J On Tue, Jun 6, 2017 at 3:27 PM, wrote: > Hi All, > I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used > as

[gmx-users] mdp options in GROMACS 4.5.5

Hi All, I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0

[gmx-users] metal ions in equilibration step

Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are two calcium ions in the protein structure. These ions play an important role. In the equilibration step,  should I consider protein,ligand and calcium ions as one single entity (for tc_grps option)? or should I

Re: [gmx-users] RMSD analysis

On 6/6/17 2:12 AM, RAHUL SURESH wrote: Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG

Re: [gmx-users] Generation of density curve for biphasic system

On 6/6/17 2:16 AM, Debraj Das wrote: Dear Justin, I am getting error with gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat It will not write anything in that file. If you want help solving this, you have to tell us exactly what the error was. I have also tried gmx

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)

On 6/6/17 2:34 AM, Apramita Chand wrote: Dear Andre, I added around 56 molecules of urea to 966 water. The peptide is just 6 residues and I just wanted to see its preferred conformations as well as hydrogen bonding. I will definitely try to extend the simulation to atleast 100ns. For the

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)

Dear Andre, I added around 56 molecules of urea to 966 water. The peptide is just 6 residues and I just wanted to see its preferred conformations as well as hydrogen bonding. I will definitely try to extend the simulation to atleast 100ns. For the equilibration, I found that the temperature and

Re: [gmx-users] RMSD Matrix Error

Dear Mark, Thanks for your reply. I think you're right about the space needed for generating RMSD Matrix. I definitely was short of 160GB !! Further, you've talked about me using highly correlated frames and that a suitable sub-sampling might solve the problem. How would I know which frames to

Re: [gmx-users] Generation of density curve for biphasic system

Dear Justin, I am getting error with gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat It will not write anything in that file. I have also tried gmx density , but it is giving the overall density profile not for the individual phase. With regards Arya Das On Mon, Jun 5,

[gmx-users] RMSD analysis

Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG analysis of complex system with that of