[gmx-users] itp file

Hi, I am surprise to see that not a single .tga ( e.g., ccl4_box.tgz) file can be open in the http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies site? Can anyone look at this matter? Re

[gmx-users] local pressure calculation

Hi, Is anyone have done local pressure calculation of a membrane by standard package gromacs-localp? Could you please show me the the .mdp file for it? Thank you very much in advance, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://

[gmx-users] mdp file to calculate local pressure

fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Sir, now, could you please tell me where I have done mistake? In the README file, it is written that it will give localpressure.dat file automatically. But I could not do it. Thank you very much for you kind help, Anirban

[gmx-users] mdp file to calculate local pressure

Dear Justin, I am using gromacs-localp of version 4.0.2. for the calculation of local pressure. But I could not understand what I should put in the mdp file. Because when I tried by the following below mdp file, it does not even create tpr file. I have tried by different options as for example

[gmx-users] mdp file to calculate local pressure

Dear Sir, I want to calculate local pressure of the membrane (pressure variation with z -axis). I am using gromacs-localp packages. As I see that all types of errors coming from saying specifically the option of WALL in .mdp file. Actually I did not understand clearly what to do in the

[gmx-users] mdp file for local pressure

Dear sir, I am calculating local pressure by gromacs-localp. My .mdp file is following integrator = sd ; stochastic dynamics -> Langevin! ld_seed = -1 ; random seed for sd dt = 0.002 ; ps ! nsteps

[gmx-users] local pressure calculation

Dear Sir, I want to calculate local pressure of the bilayer membrane. I see from the mailing list and earlier paper that it was done by gromacs-locap-3.0.2. Could you please tell me that this package will assist with gromacs 3.3.3 or gromacs 4.0.4 version. Is there any other option to c

[gmx-users] local pressure

Dear Sir, I would like to calculate local pressure of the bilayer membrane. Is it possible to do by new version of gromacs. could you please assist me to do it. After simulating bilayer m,embrane, I found trr, edr files. Thanking you , Anirban ___

[gmx-users] lateral stress and surface tension

Dear Sir, I am analysing bilayer membrane. Could you please tell me how I can calculate stress and surface tension of the membrane? Thanking you, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listi

[gmx-users] want to calculate pressure from virial

Dear Sir, I want to calculate virial, hence pressure. PV=NKT-1/3 * < sum of (r * f)> where r is displacement and f is internal force. Now, how can I proceed? 1. g_traj -f name.trr -af gives me force and each velocity with time? Now, question, is the force given in data is only

[gmx-users] introducing constrain

Dear sir, I want to put a constrain into my system. I am simulating lipid bilayer membrane by GROMACS. I want to put a virtual wall at the z-axis in my system so that no lipid can move through the virtual wall. In a code language, it is just this : for lipid :if z < 60

[gmx-users] problem in pulling in gromacs 4.03

Dear sir, I want to pull a small protein molecule (GPI) which is inserted on the upper layer of the bilayer. So, I applied pull = umbrella, where umbrella potential is used between center of mass of reference group and that of pulled group. Now, as I want to pull the protein from the li

[gmx-users] question in pulling in gromacs 4.0

Hi , I want to pull a molecule from the membrane. My complete mdp file is the following ;. ;

[gmx-users] pulling of molecule in GROMACS 4.03

Dear Sir, I want to pull a molecule called PRO from the lipid membrane DPP. To do this I have written the .mdp file as following from the help of gromacs mannual 4.0 . But when I try to make .tpr file from the .gro file, it says that "segmentation fault". Can you please wr

[gmx-users] To run in gromacs 4.0.3 in cluster

Dear Sir, In the previous older version of gromacs(3.3.x) , there is always an option -np by which I can say about the number of processors that I required parallel computation. But in the gromacs4.0.3 version, I could not find that. Can you tell me how can I run in gromacs 4.0.3 version

[gmx-users] about the run program in gromacs 4.0.3

Hi, I have run earlier in gromacs3.3.x version in parallel processor but now I have installed gromacs4.0.3. But when I want to run program in the gromacs4.0.3, it says that ... Invalid command line argument: -np

[gmx-users] about g_wham

Hi all, Could you please tell me why g_wham does not give the correct result? After doing umbrella sampling with mdrun, I got the .pdo file which is like # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group 'DPP' # Nr. of pull groups 1 # Group 1 'PIP' Umb. Pos. 3.3885

[gmx-users] Deuterium order parameter over area of membrane

Hi, I know that deuterium order parameter can be calculated by g_density but it calculate average deuterium order parameter of a type of lipid Vs. atom number of the tail of the lipid. But I want to calculate deuterium order parameter fluctuation over the area. i.e., I want to know to cal

[gmx-users] Electron density over area

Hi, I know that electron density can be calculated by g_density. But I want to calculate electron density over area of the membrane so that I can analyze the fluctuation of the electron density with the area of the membrane. Could you tell me how to do it? Thanking you, Anirban ___

[gmx-users] Thickness distribution over area of bilayer-membrane

Hi, I saw that average thickness can be measured by peak to peak distance of a electron density graph. This electron density can be calculated by g_density command. But g_density gives the average electron density of the membrane. So, I can get the average thickness of the membrane by subtract

[gmx-users] AFM by using mdrun in gromacs

Hello, I want to pull a protein from a DPPC lipid bilayer. It is written in manual that it can be done by including pull.ppa and pull.ndx with the mdrun. Now my question is how to write pull.ppa and pull.ndx.Can you tell me which parts I have to take care to make group in index

[gmx-users] deuterim order parameter

Hi, I want to analysis of the deuterium order parameter of my system containing dppc20-sm20-cholesterol20-water200tolerance3-bilayer50x50x54.pdb 0 System : 3180 atoms 1 DPPC : 1000 atomstail 14 to 31 and 32 to 50 2 SM : 1000 atoms tail

[gmx-users] about some question on gromacs

Hi, I have the following questions. Are there any other ways to make bilayer other than packmol? I want to make bilayer (.pdb file). I saw that in GROMACS, there is united atom model, then what are the GROMACS computes in the Deuterium order parameter? When I run the system for long tim

[gmx-users] about deuterium order parameter

Hello, I want to analyze the deuterium order parameter of a system contains DPPC, sphingomyelin(SM) and cholesterol(CHOL) and water(SOL). I read from the prevous mail that I have to make index file for sn1 and sn2. Now, my first question is what the meaning of sn1 and sn2 is. How can I assi

[gmx-users] How to analyze order parameter

Hi, I want to find deuterium order parameter of the system of DPPC+SM+CHOL+WATER g_order -f traj.trr -s topol.tpr -n index.ndx -dt 0.001 it gives the following error: Taking z axis as normal to the membrane Reading file topol.tpr, VERSION 3.3.3 (single precision) Using following

[gmx-users] about itp file making

Hi, This is first time that I am sending mail so I do not know the where I have to send for proper answer of my question. To make .itp file of a sugar molecule, what should be the gromacs force field (96/opls)? regards Anirban ___ gmx-users mailing l