[gmx-users] MSD and frequency of writing trajectories

Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very

Re: [gmx-users] MSD and frequency of writing trajectories

Hi, For particles that diffuse more than half a box length between frames will appear as if they haven't moved much, assuming you have periodic boundary conditions. Erik On 22 May 2013, at 11:41, Anna Akinshina anna.akinsh...@manchester.ac.uk wrote: Dear Gromacs Users, I have a question

Re: [gmx-users] MSD and frequency of writing trajectories

Sure. What's the MSD of a pendulum if you only sample at a rate equal to the period? How often you want to sample depends on the time scale of what you want to observe. That might be up to you to measure :-) Mark On Wed, May 22, 2013 at 11:41 AM, Anna Akinshina anna.akinsh...@manchester.ac.uk

[gmx-users] MSD normalization

Hi, I was just wondering how MSDs in Gromacs are normalized. I am calculatiing MSDs for my lipid system of different timesteps of simulation and I get much higher results for centre of mass calculations in comparison to mass-weighted one. And I thought about normalization issue, but I

[gmx-users] MSD

Hi, I am working on the simulation of protein memberane. How can I calculate MSD (mean squar displacement) of bond lipid ( as those phosphate atomes are written 0.35 nm of protein)? I know that I must use g_msd for calculating, but I need “index file” that is included phosphate atoms within 0.35

Re: [gmx-users] MSD

Quoting afsaneh maleki maleki.afsa...@gmail.com: Hi, I am working on the simulation of protein memberane. How can I calculate MSD (mean squar displacement) of bond lipid ( as those phosphate atomes are written 0.35 nm of protein)? I know that I must use g_msd for calculating, but I need

[gmx-users] Msd of molecule center of mass (g_msd -mol with -rmcomm)

Hello, Does anyone have additional details about how the calculations are done for the -mol flag of g_msd when using -rmcomm? I am comparing results with and without the -mol flag. I presume that when -mol is used the file specified by the -o flag contains the average msd of the centers of mass

Re: [gmx-users] msd

15:22:40 +0200 Subject: [gmx-users] msd Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box n times in x,y,z directions, repeat simulations and get a slightly different msd curves

[gmx-users] msd not linear and c.o.m removal

Hi, I am running simulations of gaseous molecules (CH4, C2H6, CO2, N2) in a silica pore (4nm in diameter), cell dimensions, 46 x 44 x 37. This in an infinite pore in the z direction. I am interested in looking at diffusion but I am a bit concerned about the shape of my MSD curves, for a

[gmx-users] msd

Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box n times in x,y,z directions, repeat simulations and get a slightly different msd curves: in the time range between 1 ps and 10 ps it flattens out

RE: [gmx-users] msd

you get the MSD per atom. Berk From: yel...@uni-mainz.de To: gmx-users@gromacs.org Date: Thu, 3 Sep 2009 15:22:40 +0200 Subject: [gmx-users] msd Hello together, i have a problem with msd. i simulate a melt of chain molecules consisting of 116 united atoms per chain. then i copy the box

[gmx-users] msd vs. time plot for molecules

Using g_msd on a group of atoms results in an msd vs. time plot which is the result of an average over all the atoms' motions. I would like to obtain the same plot, but for an average over the center of mass motions of a group of molecules. Using the -mol option results in a plot of the

Re: [gmx-users] msd and diffusion coefficient and getting unfolded trajectory

Hi, I did the calculation for water on both sides of bilayer. It is unlikely that water molecules donot cross the boundary. May be I need to wait for longer run such that molecules go out of box. I will check that. Thank you very much for your suggestions. Regards, Ananya. Ananya Debnath

[gmx-users] msd and diffusion coefficient and getting unfolded trajectory

Hi, I want to calculate MSD (mean square displacement) for DPPC-WATER bilayer system, without using g_msd tool in gromacs, but using any other code, I need a trajcetory which is unfolded. From mails in mailing list I understand that people use trjconv -pbc nojump, to remove pbc. So I used pbc

Re: [gmx-users] msd and diffusion coefficient and getting unfolded trajectory

Ananya Debnath wrote: Hi, I want to calculate MSD (mean square displacement) for DPPC-WATER bilayer system, without using g_msd tool in gromacs, but using any other code, I need a trajcetory which is unfolded. From mails in mailing list I understand that people use trjconv -pbc nojump, to

[gmx-users] MSD analysis

Dear all: I've got a DOPC/cholesterol system, and I want to get the MSD of the DOPCs near cholesterols. According to the literature, the overall movement of the each monolayer should be removed prior to the MSD analysis of individual molecules, my question is how should I do this? Thank you in

[gmx-users] MSD near specific molecules

Dear users: 1. I have a lipid bilayer of POPC with cholesterols. I'm trying to calculate the MSD of the POPCs which is nearest to cholesterols. The nearest POPCs are defined as those POPC whose C13 atoms to O6 atoms from cholesterol distances are less than a certain cutoff. Is there a good way to

Re: [gmx-users] MSD

Roman Holomb wrote: Dear colleagues, Thanks for reply! Maybe I'm doing something wrong with using g_msd . no your system is freezing. I have computed MD (5ns) for system containing 100 anion and 100 cation molecules. Results of ACFs, RDFs look good but not MSD So I have

Re: [gmx-users] MSD

Well. I think I agree with David 100 cations and 100 anions without solvent (am I correct?)... probably your system is freezing and an evidence of this is that the slope of your MSD graph tends to zero, so your D tends to zero too. But considering what you said about ACFs and RDFs, I