[gmx-users] RMSD

Hi I have 2 questions about rmsd calculation: 1) why rmsd calculation is done on heavy atoms? 2) what means of mass weighted superposition (rmsd is calculated after mass weighted superposition) Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 = Simulation Broken

Hi Lin, First of all, I would suggest sticking to a single processor until you have a protocol that works. Previously you had an issue with the addition of ions to your .top file. In your protocol, it's not mentioned. Have you made sure that issue is cleared? Cheers, Tsjerk On Sun, Jan 10,

[gmx-users] InflateGRO and trimer simulation

Hello Gromacs Users, I would like to run a simulation of a trimer in a DPPC membrane. I really like the elegant solution that inflategro script offers, however I'm afraid I won't be able to use it, because I need to have lipids in a small space between the monomers right in the center of the box

[gmx-users] time-average structure

Hi what command is useful for obtaining time-average structure? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post

[gmx-users] interaction energy

Hi I want to obtain interaction energy between protein and dna in simulation pr-dna complex. what command is suitable for that? Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] time-average structure

On 1/10/10 6:56 AM, leila karami wrote: Hi what command is useful for obtaining time-average structure? Something like g_cluster might do the trick, but be advised: http://www.gromacs.org/Documentation/Terminology/Average_Structure -Justin Any help will highly appreciated! --

Re: [gmx-users] InflateGRO and trimer simulation

On 1/10/10 5:17 AM, KM wrote: Hello Gromacs Users, I would like to run a simulation of a trimer in a DPPC membrane. I really like the elegant solution that inflategro script offers, however I'm afraid I won't be able to use it, because I need to have lipids in a small space between the

Re: [gmx-users] RMSD

leila karami wrote: Hi I have 2 questions about rmsd calculation: 1) why rmsd calculation is done on heavy atoms? 2) what means of mass weighted superposition (rmsd is calculated after mass weighted superposition) Consider the difference between centre of mass and center of geometry...

[gmx-users] InflateGRO and trimer simulation

Try the doughnut mode in the newest version of the program -- it's meant for exactly this situation. http://www.csb.bit.uni-bonn.de/inflategro.html -- original message -- Hello Gromacs Users, I would like to run a simulation of a trimer in a DPPC membrane. I really like the elegant solution

Re: [gmx-users] InflateGRO and trimer simulation

Hi, the new inflategro with the 'doughnut mode' (http://www.csb.bit.uni-bonn.de/inflategro.html) might do what you want. Ciao, Patrick Justin A. Lemkul a écrit : On 1/10/10 5:17 AM, KM wrote: Hello Gromacs Users, I would like to run a simulation of a trimer in a DPPC membrane. I really

[gmx-users] Exceeding of Maximum allowed number of DD cells

Dear GMX-Users, I'm testing my 256 full hydrated lipid on blue gene. The purpose is to find out the right number for -npme, as mdrun can not estimate itself successfully. I met the problem that how to match the maxinum allowed number for DD cells with large number of CPU cores. My simulation

Re: [gmx-users] free energy

Hello Justin, Should I add dum_opls no. in atom type file in which Lennard-jones parameters will set to zero. OR. I don't have to modify anything prog.will take care of lennard-jones interactions. I have put charge zero on all atom in TYPE B. Nilesh On Sun, January 3, 2010 12:57 pm, Justin A.

Re: [gmx-users] free energy

On 1/10/10 1:03 PM, Nilesh Dhumal wrote: Hello Justin, Should I add dum_opls no. in atom type file in which Lennard-jones parameters will set to zero. OR. I don't have to modify anything prog.will take care of lennard-jones interactions. I have put charge zero on all atom in TYPE B. You

Re: [gmx-users] InflateGRO and trimer simulation

Thank you! This is what I need, however I keep getting a lot of errors about uninitialized values. When the script finishes, the membrane is rescaled, but the protein is untouched in the corner of the new box :( I'll try to investigate a little bit despite I don't know perl, however I believe that

Re: [gmx-users] InflateGRO and trimer simulation

OK, now it works. :) Chris W dniu 10 stycznia 2010 20:06 użytkownik KM mitomas...@gmail.com napisał: Thank you! This is what I need, however I keep getting a lot of errors about uninitialized values. When the script finishes, the membrane is rescaled, but the protein is untouched in the

[gmx-users] Unstable Minimizations

I am trying to get this workflow opperational. However, my systems are getting unstable. I have preped two mdp files: 1) one for restrained 2) unrestrained. LINCS errors appear for restrained and unrestrained has infinite energy appearing.

Re: [gmx-users] Unstable Minimizations

On 1/10/10 5:18 PM, Jack Shultz wrote: I am trying to get this workflow opperational. However, my systems are getting unstable. I have preped two mdp files: 1) one for restrained 2) unrestrained. LINCS errors appear for restrained and unrestrained has infinite energy appearing.

[gmx-users] Retinal and Schiff base parameters for ffG53a6

Hello, I would like to simulate bacteriorhodopsin embedded into a membrane. I think ffG53a6 is a good choice - force field is quite new (at least newer than ffgmx) and there are topologies available for the most popular lipids, for example the set developed by Andreas Kukol. To run a simulation I

Re: [gmx-users] Retinal and Schiff base parameters for ffG53a6

On 1/10/10 6:16 PM, KM wrote: Hello, I would like to simulate bacteriorhodopsin embedded into a membrane. I think ffG53a6 is a good choice - force field is quite new (at least newer than ffgmx) and there are topologies available for the most popular lipids, for example the set developed by

Re: [gmx-users] free energy

Thanks Justin, I am not setting any Lennard-Jones parameters to zero for part B. I put zero charge on all atoms for Part B. (Lennard Jones parameters for B are same as Part A). I am using default parameters for couple-lambda0 and couple-lambda1. For one of my simulation (glucose + ionic

Re: [gmx-users] Exceeding of Maximum allowed number of DD cells

Chao Zhang wrote: Dear GMX-Users, I'm testing my 256 full hydrated lipid on blue gene. The purpose is to find out the right number for -npme, as mdrun can not estimate itself successfully. I met the problem that how to match the maxinum allowed number for DD cells with large number of CPU

Re: [gmx-users] free energy

On 1/10/10 7:02 PM, Nilesh Dhumal wrote: Thanks Justin, I am not setting any Lennard-Jones parameters to zero for part B. I put zero charge on all atoms for Part B. (Lennard Jones parameters for B are same as Part A). Under Gromacs 4.0.x, you should be able to leave the topology alone

Re: [gmx-users] free energy

Justin, Here I have pasted the data about free energy from mdout.mdp file ; Free energy control stuff free_energy = yes init_lambda = 0.20 delta-lambda = 0 sc-alpha = 0.6 sc_power = 1 sc-sigma = 0.3

Re: [gmx-users] free energy

On 1/10/10 7:53 PM, Nilesh Dhumal wrote: Justin, Here I have pasted the data about free energy from mdout.mdp file ; Free energy control stuff free_energy = yes init_lambda = 0.20 delta-lambda = 0 sc-alpha = 0.6 sc_power =

Re: [gmx-users] Unstable Minimizations

Thanks Justin, I went back to the original pdb files. These were conformations of the same protein derived from molecular dynamics simulations performed by Andrey. What I intially attempted was preping the structures using tleap, hoping to paint in missing atoms for residues. Then use this to

Re: [gmx-users] Unstable Minimizations

On 1/10/10 9:47 PM, Jack Shultz wrote: Thanks Justin, I went back to the original pdb files. These were conformations of the same protein derived from molecular dynamics simulations performed by Andrey. What I intially attempted was preping the structures using tleap, hoping to paint in