Re: [gmx-users] pulling protein-ligand complex

Alright. I'm attaching md_pull.mdp and sumary_distances.dat file. May be I have set pulling rate very low. Anyway have a look. On Sun, Jan 8, 2017 at 6:03 AM, Justin Lemkul wrote: > > > On 1/7/17 5:20 PM, abhisek Mondal wrote: > >> It finished normally then. I got another

[gmx-users] LJ Interaction between 2 groups looks unusual

Dear gmx users, I run 500 ns simulation using GPU. After simulation I made mdrun -rerun. Finally, I performed gmx energy analysis. Result looks unusual as a following figure. LJ Interaction between 2 groups. ​ How is the figure? Is there any advice? Best regards, Mijiddorj -- Gromacs Users

Re: [gmx-users] Regarding gromacs commands..

can i create it with Avogadro molecular editor software..?? I tried creating using this software,, than if i compile it and run the command of mdrun.. it is giving segmentation fault how to rectify it..?? Sent with Mailtrack

Re: [gmx-users] Topology parameters for ligand

Thank you for your reply In last section of your tutorial you have suggested some changes to made in mdp file. That can be used for solvation free energies. For free energy calculation of protein drug complex, is it only lambda restraint to be defined? On 8 Jan 2017 01:45, "Justin Lemkul"

Re: [gmx-users] pulling protein-ligand complex

On 1/7/17 5:20 PM, abhisek Mondal wrote: It finished normally then. I got another question. I was pulling along XZ plane. Distances I got is not a arithmetic progression with respect to different configurations. I mean the output looks like: 50 1.3637913 51 1.3729873 52 1.4363521 53 1.4652436

Re: [gmx-users] pulling protein-ligand complex

It finished normally then. I got another question. I was pulling along XZ plane. Distances I got is not a arithmetic progression with respect to different configurations. I mean the output looks like: 50 1.3637913 51 1.3729873 52 1.4363521 53 1.4652436 54 1.4503893 55 1.4260585 56 1.3836564 57

Re: [gmx-users] pulling protein-ligand complex

On 1/7/17 3:59 PM, abhisek Mondal wrote: yes. 19 and 20. I have been able to modify distances.pl and it is running well I guess. It is taking a little time per configuration to process. Is there any way to know if distances.pl program terminates normally and calculations are successful ?

Re: [gmx-users] pulling protein-ligand complex

yes. 19 and 20. I have been able to modify distances.pl and it is running well I guess. It is taking a little time per configuration to process. Is there any way to know if distances.pl program terminates normally and calculations are successful ? On Sun, Jan 8, 2017 at 2:20 AM, Justin Lemkul

Re: [gmx-users] pulling protein-ligand complex

On 1/7/17 3:36 PM, abhisek Mondal wrote: Alright, I'm trying. Please tell me one thing, given the fact I want to analyse the protein-ligand pull scenario, what should be my choice during the prompt i get after executing "g_dist_mpi -s pull.tpr -f conf200.gro -n index.ndx -o all" Reading file

Re: [gmx-users] pulling protein-ligand complex

Alright, I'm trying. Please tell me one thing, given the fact I want to analyse the protein-ligand pull scenario, what should be my choice during the prompt i get after executing "g_dist_mpi -s pull.tpr -f conf200.gro -n index.ndx -o all" Reading file pull.tpr, VERSION 4.6.2 (single precision)

Re: [gmx-users] pulling protein-ligand complex

On 1/7/17 3:24 PM, abhisek Mondal wrote: So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2. If you're using an old version, the syntax is totally different, so you will have to make lots of changes to the script (or not use it at all). The catch here to analyze the COM

Re: [gmx-users] pulling protein-ligand complex

So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2. The catch here to analyze the COM distances between 2 pull groups. Am I getting that right ? On Sun, Jan 8, 2017 at 1:46 AM, Justin Lemkul wrote: > > > On 1/7/17 2:51 PM, abhisek Mondal wrote: > >> Hi, >> I'm

Re: [gmx-users] pulling protein-ligand complex

On 1/7/17 2:51 PM, abhisek Mondal wrote: Hi, I'm pulling ligand out of protein using umbrella sampling method in gromacs-4.6.2. Using "trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep" command generated 500 different files (selected "SYSTEM" in interactive prompt, need to study protein and

Re: [gmx-users] Topology parameters for ligand

On 1/7/17 6:05 AM, tasneem kausar wrote: Dear all I am following Justin's tutorial methane in water for free energy calculation. I am using Gromacs-5.1.4. The charges of methane in topology are set to zero. So following the same protocol, is it relevant to set the charges at zero in topology

Re: [gmx-users] REg MD results

On 1/7/17 5:14 AM, Parul Raj Srivastava wrote: I have given an MD run for a quaternary protein structure by taking 2 chains at a time for the MD run.The rmsf graph so obtained is showing erratic behaviour,please find attached graph.Is this result justified or incorrect?? The list does not

Re: [gmx-users] Gromacs Simulation Question

On 1/6/17 5:14 PM, Academic Research wrote: Hello everyone, I have computationally designed several synthetic proteins that are not found in nature. My lab has limited resources for wet lab work and so I would like to use gromacs to simulate these proteins in water and see weather they

[gmx-users] pulling protein-ligand complex

Hi, I'm pulling ligand out of protein using umbrella sampling method in gromacs-4.6.2. Using "trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep" command generated 500 different files (selected "SYSTEM" in interactive prompt, need to study protein and ligand simultaneously). But when I use "perl

[gmx-users] Topology parameters for ligand

Dear all I am following Justin's tutorial methane in water for free energy calculation. I am using Gromacs-5.1.4. The charges of methane in topology are set to zero. So following the same protocol, is it relevant to set the charges at zero in topology of the drug. I am confused because in

[gmx-users] REg MD results

I have given an MD run for a quaternary protein structure by taking 2 chains at a time for the MD run.The rmsf graph so obtained is showing erratic behaviour,please find attached graph.Is this result justified or incorrect?? Regards, Parul Raj Srivastava, M.Tech.Computational Biology, Anna