Re: [gmx-users] Diffusion/PBC

Hi Debashis, Makes sure that the anion and receptor are together in the reference structure you use for trjconv -pbc nojump Cheers, Tsjerk On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu debashis.sah...@gmail.comwrote: Dear All, I have an problem related to jumping trajectory.

Re: [gmx-users] Diffusion/PBC

Your best bet is probably to center everything on the receptor. That will prevent jumping of the receptor only, which is hopefully all you need. -Trayder On Tue, Nov 5, 2013 at 7:14 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Debashis, Makes sure that the anion and receptor are

[gmx-users] Diffusion/PBC

Dear All, I have an problem related to jumping trajectory. In my MD run, there is a receptor molecule which is binding with an halogen anion in water solvent. In the original trajectory, the binding between them looks fine but jumping present. To remove the jumping of the system from

[gmx-users] diffusion constant level off

Dear users, I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration, RMSD matrix. This simulation has

Re: [gmx-users] Diffusion beyond periodic boundary

Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would

Re: [gmx-users] Diffusion beyond periodic boundary

...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Date: 2013-02-09 17:24:23 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM

Re: [gmx-users] Diffusion beyond periodic boundary

Date: 2013-02-09 17:24:23 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, You can remove the jumps/rewinds using 'trjconv -pbc nojump'. Cheers, Tsjerk On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote: Dear All I have

Re: [gmx-users] Diffusion beyond periodic boundary

:17:12 Subject: Re: [gmx-users] Diffusion beyond periodic boundary Hi Kenji, That's not possible. But why would you need that? It's not very hard to make the changes required in gmx_trjconv.c Cheers, Tsjerk On Sat, Feb 9, 2013 at 9:37 AM, Kenji Mochizuki kmo...@ims.ac.jp wrote

[gmx-users] Diffusion beyond periodic boundary

Dear All I have performed MD run with periodic boundary condition, which system is consist of water and LJ particles. I would like to know the time dependence of the dislocated distance (diffusion) from the starting time (t=0). Firstly, I made pdb file of the trajectory, then calculated the

[gmx-users] diffusion

Desr Gromacs Users, I have several systems consist of: surfactants, solvent, and additives molecules in several concentrations. I want obtain extent of movement each of materials in the mixture in different concentrations. Is the self-diffusion coefficient good foe this? I have doubt about

[gmx-users] diffusion coeffecient/constant

Hi, I am working with DOPC lipid molecules, I was searching the literature for the value of the diffusion coeffecient for DOPC. I could not find one. can some one tell me what the value is is it close to (8.6 ± 0.2) × 10−12 m2/s? Ramya Parthasarathi ramya.sar...@aol.com -- gmx-users

Re: [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

On 12/10/11 3:23 AM, Matthew Zwier wrote: Hi Ruhollah, A while ago on the list there was a discussion of extreme memory use and possibly-incorrect results from g_msd under some conditions. The problem could be worked around by imaging the trajectory with trjconv first to remove jumps across

[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

David, thank you for your reply. but, g_msd gives a diffusion coefficient which is one order of magnitude higher than expected for a small polypeptide (15 res long with gyration Rg ~ 0.8nm) with the same size. this is command line i used: g_msd-mpi -f md_mine_2nd.xtc -s md_mine_2nd.tpr -o

Re: [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

Hi Ruhollah, A while ago on the list there was a discussion of extreme memory use and possibly-incorrect results from g_msd under some conditions. The problem could be worked around by imaging the trajectory with trjconv first to remove jumps across the box, then running g_msd on the results.

[gmx-users] diffusion coefficient

I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goes out of the right side it comes in from left side, which leads to an artificial

Re: [gmx-users] diffusion coefficient

On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goes out of the right side

Re: [gmx-users] diffusion coefficient

On 2011-12-09 08:34, Mark Abraham wrote: On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote: I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when

[gmx-users] diffusion of the water at the micelle surface

that this option exist in gromacs. Unfortunately, it is not the case, so i will try your suggestions . Stephane -- Message: 6 Date: Sat, 26 Nov 2011 10:17:10 -0500 From: chris.ne...@utoronto.ca Subject: [gmx-users] diffusion of the water at the micelle surface To: gmx

[gmx-users] diffusion of the water at the micelle surface

in gromacs. Unfortunately, it is not the case, so i will try your suggestions . Stephane -- Message: 6 Date: Sat, 26 Nov 2011 10:17:10 -0500 From: chris.neale at utoronto.ca Subject: [gmx-users] diffusion of the water at the micelle surface To: gmx-users at gromacs.org

[gmx-users] diffusion of the water at the micelle surface

When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something similar. I doubt that the standard gromacs tools will do this

Re: [gmx-users] diffusion of the water at the micelle surface

On Sat, Nov 26, 2011 at 11:17 PM, chris.ne...@utoronto.ca wrote: When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something

[gmx-users] diffusion through nanotube

Hello, I am studying the diffusion of a small molecule through a cyclic peptide based nanotube using pull code, here is my code for pulling, pull= umbrella pull_geometry = position pull_vec1 = 0 0 1 pull_start = yes pull_ngroups= 1 pull_group0 = Protein

[gmx-users] Diffusion Coefficient

Hi I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s) But, the experimental data is around 1x1e-6 (cm2/s). How could I explain for this discrepency? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] Diffusion Coefficient

Chih-Ying Lin wrote: Hi I calculated the diffusion coefficient for lysozyme and get ~4x1e-6 (cm2/s) But, the experimental data is around 1x1e-6 (cm2/s). How could I explain for this discrepency? If the simulation is based off of a simulation of a single lysozyme protein in water, I'd be

[gmx-users] diffusion constant

Hello, I am trying to calculate the diffusion coefficient of a molecule in water using g_msd, and I have a doubt: I get 3 different values when I use the trajectory directly from the simulation, the trajectory using PBC conditions, and the fitted trajectory. Which would be the correct value for

[gmx-users] diffusion coefficients

Hello, I'm investigating the diffusion coefficient of gases in liquids. Therefore, I insert some molecules with the genbox tool in an equilibrated system. After a NPT run to adjust the density, I'm running an NVT simulation to calculate the diffusion coefficient (g_msd). MSD of the liquids are

[gmx-users] Diffusion constant

Dear Users I want to calculate the diffusion constant of one molecule in water.I make this calculation in the followin way: Obtaining a continuos trajectory 1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc Obtaining the msd of the solute, removing the center of mass of the system Firt way:

[gmx-users] diffusion coefficient of oxygen

Respected Experts I need your help In my study of diffusion of a oxygen molecule in 255 molecules of water, I previously used SPC water model with ffgmx force field with cutoff L-J and Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for diffusion coefficient of

Re: [gmx-users] diffusion coefficient of oxygen

Sunil Thapa wrote: Respected Experts I need your help In my study of diffusion of a oxygen molecule in 255 molecules of water, I previously used SPC water model with ffgmx force field with cutoff L-J and Coulomb interaction. I wanted to reproduce the experimental value 2.4 unit for

RE: [gmx-users] diffusion coefficient of oxygen

diffusion coefficient and it combines well with the Gromos force fields, so use that. It is well known that the diffusion of SPC is twice what it should be. Berk Date: Wed, 10 Mar 2010 07:35:41 -0500 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] diffusion

[gmx-users] diffusion coefficient of oxygen molecule

Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between water and oxygen. I

Re: [gmx-users] diffusion coefficient of oxygen molecule

Sunil Thapa skrev: Respected experts I want to calculate the self diffusion cofficient of an oxygen molecule in water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones interaction between

Re: [gmx-users] diffusion coefficient of oxygen molecule

Hi, If i remember correctly SPC/E water might be worth trying. There is plenty of research paper in this field. Try this paper http://pubs.acs.org/doi/abs/10.1021/jp003020w Also P,T coupling have effects on Diffusion Coeff. amit On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa mephy...@yahoo.com

[gmx-users] diffusion coefficient

Hi Everyone, I have been trying to calculate diffusion coefficient for water. I am trying to reproduce the numbers published in journal papers. I am using SPCE water model. I use the g_msd analysis tool. g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8 I use a box of volume 6x6x6 nm^3 which

Re: [gmx-users] diffusion coefficient

Hi, you already have your solution at hand. On 10.02.2010, at 10:05, Amit Choubey wrote: Hi Everyone, I have been trying to calculate diffusion coefficient for water. I am trying to reproduce the numbers published in journal papers. I am using SPCE water model. I use the g_msd analysis

Re: [gmx-users] diffusion coefficient

10 ps is too short of a trajectory, even for such a large system (for pure water it is considered large). i would guess that it is a typing-error and you ran for 10 ns? omer. On Wed, Feb 10, 2010 at 11:05, Amit Choubey kgp.a...@gmail.com wrote: I use a box of volume 6x6x6 nm^3 which has 7161

[gmx-users] Diffusion by g_msd

Dear All, I was trying to calculate diffusion of water molecule in a membrane channel protein by g_msd utility of gromacs. First I have identified channel waters which reside inside the channel for 500ps (5000ps-5500ps simulation time). Letter I have made a index file specifying these water

[gmx-users] Diffusion of Ammonia Gas

Dear GROMACS-ites, I am trying to determine whether OPLS can be used to model gas-phase ammonia. To this end, I created a 30 nm^3 box with 729 ammonia molecules in it, performed energy minimization, and ran a simulation at 298K 1.01325 bar for 20 ps followed by another simulation of 20 ps

Re: [gmx-users] Diffusion of Ammonia Gas

Darrell Koskinen wrote: Dear GROMACS-ites, I am trying to determine whether OPLS can be used to model gas-phase ammonia. To this end, I created a 30 nm^3 box with 729 ammonia molecules in it, performed energy minimization, and ran a simulation at 298K 1.01325 bar for 20 ps followed by

[gmx-users] Diffusion coefficient depenting on time interval

Hi users, I have simulated a box of NVT-water, more specifically the flexible urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987). What I notice is that the diffusion coefficient increases when I calculate it from a longer snippet from my trajectory. If I use only 100 ps;

Re: [gmx-users] Diffusion coefficient depenting on time interval

Erik Marklund wrote: Hi users, I have simulated a box of NVT-water, more specifically the flexible urey-bradley-like TIPS-reparametrisation by Dang and Pettitt (1987). What I notice is that the diffusion coefficient increases when I calculate it from a longer snippet from my trajectory. If I

[gmx-users] diffusion, g_msd and trestart

Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx I get a list of diffusion coefficients - one for each glycine molecule. I then calculate the average

Re: [gmx-users] diffusion, g_msd and trestart

Enemark Soeren wrote: Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx I get a list of diffusion coefficients – one for each glycine molecule. I

RE: [gmx-users] diffusion, g_msd and trestart

Date: Mon, 27 Jul 2009 11:12:16 +0200 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box

RE: [gmx-users] diffusion, g_msd and trestart

-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: Dear all

RE: [gmx-users] diffusion, g_msd and trestart

-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: Dear all

Re: [gmx-users] diffusion, g_msd and trestart

Enemark Soeren wrote: -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark

Re: [gmx-users] diffusion coefficient with g_msd

On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at

SV: [gmx-users] diffusion coefficient with g_msd

:34 Til: Discussion list for GROMACS users Emne: Re: [gmx-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate

Re: SV: [gmx-users] diffusion coefficient with g_msd

-users] diffusion coefficient with g_msd On Jun 4, 2009, at 4:18 PM, Sarah Witzke wrote: Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside

SV: SV: [gmx-users] diffusion coefficient with g_msd

Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have posted my .mdp file

Re: SV: SV: [gmx-users] diffusion coefficient with g_msd

Sarah Witzke wrote: Fra: gmx-users-boun...@gromacs.org på vegne af XAvier Periole Sendt: fr 05-06-2009 13:32 Til: Discussion list for GROMACS users Emne: Re: SV: [gmx-users] diffusion coefficient with g_msd Sarah Witzke wrote: Dear XAvier, Thank you very much for your answer. I have

[gmx-users] diffusion coefficient with g_msd

Dear gromacs users, I have done several simulations with small lipophilic, molecules diffusing into a DMPC bilayer. I would like to calculate the diffusion coefficient of the molecules inside the membrane, and therefore I looked at g_msd. The manual (version 4.0) states on p. 250 (manual

Re: [gmx-users] Diffusion coefficients ( Exp X Simul )

Subject: Re: [gmx-users] Diffusion coefficients ( Exp X Simul ) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 49ada3f0.4090...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed Eudes Fileti wrote: Hello, someone could suggest me references which

Re: [gmx-users] Diffusion coefficients ( Exp X Simul )

compounds and mixtures. Water is off more than the other molecules IIRC. eef Message: 6 Date: Tue, 03 Mar 2009 22:41:04 +0100 From: David van der Spoel sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Diffusion coefficients ( Exp X Simul

Re: [gmx-users] Diffusion coefficients ( Exp X Simul )

See also the work of Hummer (JPC-B (2004), http://dx.doi.org/10.1021/jp0477147), dealing with box size effect on D. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Tue, Mar 3, 2009 at 23:37, Eudes Fileti fil...@ufabc.edu.br

[gmx-users] Diffusion coefficients ( Exp X Simul )

Hello, someone could suggest me references which discusses the difficulty of obtaining values for diffusion coefficients in agreement to the experimental values? For water that is well known, but I do not know of any reference that discusses this topic Thanks eef

Re: [gmx-users] Diffusion coefficients ( Exp X Simul )

Eudes Fileti wrote: Hello, someone could suggest me references which discusses the difficulty of obtaining values for diffusion coefficients in agreement to the experimental values? For water that is well known, but I do not know of any reference that discusses this topic You mean that

[gmx-users] diffusion of oxygen in water

RESPECTABLE EXPERTS   HAPPY NEW YEAR   I am a beginner in gromacs. I want to know if it is possible to study the diffusion of oxygen (as solute ) gas in water (solvent) with the current features of gromacs.   Does gromacs present the required forcefields? How can I make the corresponding pdb

Re: [gmx-users] diffusion of oxygen in water

Sunil Thapa wrote: RESPECTABLE EXPERTS HAPPY NEW YEAR Please don't use all capitals - it's the internet equivalent of shouting. I am a beginner in gromacs. I want to know if it is possible to study the diffusion of oxygen (as solute ) gas in water (solvent) with the current features of

Re: [gmx-users] Diffusion Cofficient of POPC

On Wed, 16 Jul 2008 07:18:17 +0200 Jojart Balazs [EMAIL PROTECTED] wrote: Dear Minnale, As far as i know, at least 100ns simulation should be performed in order to obtain the correct diffusion coefficient for lipids. I think, if you performed 5 ns it is too short. I am not sure about that!

[gmx-users] Diffusion coefficients

Hi to everybody! I wanted to ask to you your opinion... I've computed the diffusion coefficient of a aqueous solution solution of Cd(2+) both with g_msd and g_velacc. I'have obtained a diff coeff of about 0.64 10^-5 cm^2/s and 0.71 10^-5 cm^2/s for two different water models (respectively SPC/E