[gmx-users] Effect of compilers loaded at runtime

Hi, I'm wondering if the version of the intel toolchain loaded when calling mdrun affects results? My gromacs version was compiled with intel/2015b - would it matter if module intel/2016b was loaded at runtime? Thanks Dries -- Gromacs Users mailing list * Please search the archive at

[gmx-users] modeling CNT, center of mass velocity, energy minimization

Hi GROMACS users,   I have some questions:   1-  Can I model a carbonnanotube (CNT) conveying fluid in GROMACS subjected to a magnetic field? 2-  How can I check the centerof mass velocity of my system? 3-  I want to calculate volumeand water self diffusion

Re: [gmx-users] umbrella simulation PMF curve

Your umbrellas are not well spaced. There is a gap at 1.2, 2.25 and around 4.4 which is affecting your pmf profile. Add more simulations at those points and re-check again. Regards, Sarath On 22 February 2016 at 11:09, Nikhil Maroli wrote: > Hello , > > can anyone tell

[gmx-users] umbrella simulation PMF curve

Hello , can anyone tell me why im getting profile like this after umbrella simulation im attaching both hist.xvg and profile.xvg plot histo plot https://drive.google.com/file/d/0BxaQk_pcR9viaGRNQlhrcVVmazQ/view?usp=sharing profile

Re: [gmx-users] fix COM

Thank you Mark, Could you please help to give more instructions on how to generate restraints on a centre of mass virtual site? I know genrestr can implement restraints, but I have no idea how to set a virtual site. BTW: is the latest version suitable for mpt 2.13? it seems that version

Re: [gmx-users] fix COM

Hi Justin, Thanks for your information. My atom group contains only 3 atoms, each of which is on one chain of a triple helix. Flat-bottomed is new for me. I went through section 4.3.2 in the manual, but still feel confused about how to get the parameters and how to apply constraints. Do you

Re: [gmx-users] fix COM

Or probably on a centre of mass virtual site. Mark On Sun, 21 Feb 2016 21:27 Justin Lemkul wrote: > > > On 2/20/16 10:44 PM, Ming Tang wrote: > > Dear Gromacs experts, > > > > Is there a approach to fix the centre of mass of a group of atoms only > without fixing all of the

Re: [gmx-users] Potential energy

Thank you Justin, do you know how I can find or modify the center of mass velocity of my system? On Sunday, February 21, 2016 11:50 PM, Justin Lemkul wrote: On 2/21/16 3:15 PM, mohammad r wrote: > Hi everybody, > > > > Is it correct to say the potential energy after

Re: [gmx-users] fix COM

On 2/20/16 10:44 PM, Ming Tang wrote: Dear Gromacs experts, Is there a approach to fix the centre of mass of a group of atoms only without fixing all of the atoms during a stretching process? No, but you can approximate such behavior using a flat-bottom position restraint on judiciously

Re: [gmx-users] position restraints for different protein atoms

On 2/20/16 11:16 PM, Irem Altan wrote: Hi, Is there a way to generate position restraint files such that the main chain atoms and the side chain atoms have different force constants? Similarly, Yes, you can invoke genrestr with a suitable index group for whatever part of the protein you

Re: [gmx-users] docking

On 2/21/16 4:14 AM, Negar Parvizi wrote: Thank you so much for your help. Should I use protein-ligand complex tutorial for MD simulation of docked complexes? Unless the "ligand" is a polypeptide or some other biological molecule that is described in the force field, yes, that's pretty

Re: [gmx-users] Embedding Protein into lipid bilayer

On 2/21/16 5:44 AM, khourshaeisha...@mech.sharif.ir wrote: p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Justin first of all, thanks for your replay. but I should cite that the bizarre character that you saw in my Email was Sharif university Email

Re: [gmx-users] umbrella simulation -pulling in other directions

On 2/21/16 8:28 AM, Nikhil Maroli wrote: Dear all, i am doing Umbrella sampling,as my ligand is in x axis after i made a box,so i have to pull it towards -x direction instead of z which mention in tutorial, can i give pull_coord1_rate= -0.01 negative rate? is it make any sense or is

Re: [gmx-users] Potential energy

On 2/21/16 3:15 PM, mohammad r wrote: Hi everybody, Is it correct to say the potential energy after energyminimization should be negative and in the order of 105-106 ?according to gromacs tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html

[gmx-users] Potential energy

Hi everybody,   Is it correct to say the potential energy after energyminimization should be negative and in the order of 105-106 ?according to gromacs tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html Thank you, Mohammad. -- Gromacs Users

Re: [gmx-users] converted topology from amber to gromacs

Thank you very much Justin On Saturday, February 20, 2016 10:53 PM, Justin Lemkul wrote: On 2/20/16 8:49 AM, mohammad r wrote: > Hi Justin, > > Thank you for your answer, I used grompp and it didn't give me error. I've > attached a topology file of my systems. Can

[gmx-users] Screenshot from 2016-02-21 18:45:00.png

I've shared an item with you: Screenshot from 2016-02-21 18:45:00.png https://drive.google.com/file/d/0BxaQk_pcR9viTURiNWVJR3NfS3M/view?usp=sharing=CLDlkagE=56c9bb79 It's not an attachment -- it's stored online. To open this item, just click the link above. -- Gromacs Users mailing list *

[gmx-users] umbrella simulation -pulling in other directions

Dear all, i am doing Umbrella sampling,as my ligand is in x axis after i made a box,so i have to pull it towards -x direction instead of z which mention in tutorial, can i give pull_coord1_rate= -0.01 negative rate? is it make any sense or is there any ohter method to pull in -X direction

[gmx-users] Embedding Protein into lipid bilayer

p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Justin first of all, thanks for your replay. but I should cite that the bizarre character that you saw in my Email was Sharif university Email domains fault not me. also different copies of Email was because of