[gmx-users] Issue with number of cores

Dear Gromacs users I want to do a mdrun on my system which has 7 cores but I just want to use 5 of them. Is there anyway to use 5 of them without effecting on the remained ones ? I have used the remained ones with another software before. I really appreciate it if� you can

[gmx-users] Compressibility in .mdp

Dear Gromacs users I have a question about the concept of the compressibility factor in .mdp file. suppose I assign Compressibility in X direction equal to zero. does this mean that the atoms in X direction cannot move at all or just the size of the� simulation box� in this

[gmx-users] Paradox in .mdp parameter value between Justin's tutorial and martini's one

pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Gromacs user Im currently working with Coarse grain martini forcefield, but before that Ive used all atom simulation. in the below suggested .mdp file [1] , as

[gmx-users] Adaptive Biasing Force method

Dear GROMACS users Is there any way� to employ the adaptive biasing force (ABF) method with GROMACS ?! If so,� could you please introduce me a tutorial or article about it ? I really appreciate it. best regards, Ali == Ali khourshaei shargh

[gmx-users] Output of g energy

Dear Justin thanks for your response. so the negetive amount of pressure x-x is the component of the stress tensor along the x-axis in mechanical engineering, right ? thans in advance. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] NEMD

Dear Mark, Thanks for your response. actually I did it by posting question with the subject " Relaxation Test " but unfortunately nobody gave me any kind of feedback. so could you please that question to see if you can help me? thanks in advance. == Ali khourshaei shargh

[gmx-users] Output of g energy

Dear GROMACS user I have a question about the output of g energy. what is exactly the meaning of Pressure x-x ? is it the same as the stress in mechanical engineering or not ?! best regards, Ali == Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical

[gmx-users] NEMD

Dear Gromacs users I am a M.Sc student at Sharif university in field of mechanical engineering. for my M.Sc thesis I'm using GROMACS and for a part of it, I need to use NEMD. I searched Internet but unfortunately found nothing related to gromacs ( I mean Example, article and ...). So could anyone

[gmx-users] Relaxation Test

Dear GROMACS user During the last 3 weeks, I confront with a really though problem through my M.Sc thesis. I don't now if you are familiar with Relaxation test in Mechanical Engineering or not, simply It is a test In which we exert a constant strain to a simulation box and monitor its Stress

[gmx-users] problem with MPI,thread and number of CPU

p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear Gromacs users During simulating DPPC membrane I confront with several Problems. I intend to express them here and I really appreciate it if you help me. Briefly I started to simulate a DPPC containing 2000 W and

[gmx-users] Extend to Embedding a protein into a lipid box using CGMD

Dear all based on my last question, consider My simulation box file is md.gro and my protein is CG.gro. now if you can, please write the desired command for me to embed this two file and have a lipid bilayer membrane embedded with protein please. best regards

[gmx-users] Embedding a protein into a lipid box using CGMD

Dear all during a part of martini tutorial it says: If a stable DPPC membrane with the wanted box dimensions is already available,�genbox�will be able to insert the peptides in the bilayer (the peptides have to be pre-centered and positioned to ensure their presence inside

[gmx-users] Coarse grain membrane simulation of DPPC

Dear all Recently I saw� an article about 128DPPC� of lipid bilayer. it says that the bilayer would rupture by a lateral 200bar tension, using Gromacs all atom. now I want to gain that using coarsegrain method. for all atom the pdb file is obtainable but for CG, I built it

[gmx-users] Coarse Grain using martinize.py

Dear all I want to simulate a system of 128 DPPC with 3655 water molecule which its .pdb file is available on professor tielman website. I want to Coarse grain it but apparently at first i should turn the pdb file into appropriate type for using with martini. I understood, I should use marti

[gmx-users] Embedding Protein into lipid bilayer

Dear Justin Thanks for your reply. I think, I got what you mean. By the way, My protein needs to use BGL residue and of course this type of the residue isnt available in the gromacs sources. So I find its information in ATP site and it is attached to my Email as a .itp file.

[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

[gmx-users] A question to Justin about his helpful tutorial

pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Dear justin after finishing your tutorial, I tried to embed 1r2h protein into lipid bilayer. when I tried to use pdb2gmx� via "gmx pdb2gmx -f 2rh1.pdb -o

[gmx-users] Embedding Protein into lipid bilayer

t;> before using it in pdb2gmx command or the GROMACS cant >> keep on and will be died with a fatal error ( something like adding cope >> to the ends of the protein ). could >> somebody please tell me what should I do ? by the way I found out that >> Justins >> tutori

[gmx-users] Embedding Protein into lipid bilayer

pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom: 0.1in; line-height: 120%; }a:link { } Hi Catarina Thanks for your reply, I really appreciate it. you know, I complete Justins Tutorial, so I know what procedures I should do. but now I want to embed 2rh1

[gmx-users] (no subject)

Dear All During researching Internet, I found justin and Anirbans tutorial about embedding protein in lipid membrane. It was useful and I appreciate them but I had one question. as I understood, I should make some changes to protein pdb file ( 1r2h for Ex) before using it in pdb2gmx command

[gmx-users] Embedding Protein into lipid bilayer

Dear All During researching Internet, I found justin and Anirbans tutorial about embedding protein in lipid membrane. It was useful and I appreciate them but I had one question.

[gmx-users] Embedding Protein into lipid bilayer

Dear All During researching Internet, I found justin and Anirbans tutorial about embedding protein in lipid membrane. It was useful and I appreciate them but I had one question. as I understood, I should make some changes to protein pdb file ( 1r2h for Ex) before using it in pdb2gmx command

[gmx-users] Gromacs issue

Dear All I have a quick question about GROMACS. Is there any chance to exert different types of loading such as torsional or bending or linear tension loading on simulation box in GROMACS ? Best wishes Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical Engineering

[gmx-users] Gromacs issue

Dear All I have a quick question about GROMACS. Is there any chance to exert different types of loading such as torsional or bending or linear tension loading on simulation box in GROMACS ? Best wishes Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical

[gmx-users] Question about GROMACS

Dear All I have a quick question about GROMACS. Is there any chance to exert different types of loading such as torsional or bending or linear tension loading on simulation box in GROMACS ? Best wishes Ali khourshaei shargh (khourshaeisha...@mech.sharif.edu) Department of Mechanical