Re: [gmx-users] density profile

On 3/31/13 1:12 PM, Elisabeth wrote: Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cp

Re: [gmx-users] density profile

Thanks Justin for your reply. To avoid compressing down the cell I thought using semiisotropic option with 0 compressibility in Z would be appropriate. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I ex

Re: [gmx-users] density profile

On 3/31/13 12:27 PM, Elisabeth wrote: Thank Justin. I am interested in the density profile at the solvent-air interface. I wanted to see how density changes with position at different pressures...I have the equilibrated boxes at several pressures obtained from NPT but I am not sure whether runn

Re: [gmx-users] density profile

Thank Justin. I am interested in the density profile at the solvent-air interface. I wanted to see how density changes with position at different pressures...I have the equilibrated boxes at several pressures obtained from NPT but I am not sure whether running g_density on the current simulations c

Re: [gmx-users] density profile

On 3/31/13 11:41 AM, Elisabeth wrote: Dear all, In order to get density profile of a pure system the box has to get extended in one drection (e.g Z) as we do for surface tension calculations or density profile can be also obtained from the usual box filled up with the molecules without need fo

[gmx-users] density profile

Dear all, In order to get density profile of a pure system the box has to get extended in one drection (e.g Z) as we do for surface tension calculations or density profile can be also obtained from the usual box filled up with the molecules without need for empty space in Z Thanks for any comment

Re: [gmx-users] Density measurment

On 10/3/12 12:22 AM, rama david wrote: Thank you Justin for your reply , I tried g_density again after your reply. But I found that it give density with respect to box dimension and not to time. I suggested before that you could perhaps advantageously using the -b and -e flags to achieve s

Re: [gmx-users] Density measurment

Thank you Justin for your reply , I tried g_density again after your reply. But I found that it give density with respect to box dimension and not to time. g_densmap have xpm output and no the xvg ( I need density or no of water molecule present in between two peptides with respect to the time

Re: [gmx-users] Density measurment

On 10/2/12 7:07 AM, rama david wrote: Hi Gromacs Users, I did simulation of two random coil peptides for 100ns. after 70 ns these peptide get converted to anti parallel beta sheet structure. I am interested to see the water density in between these peptideswith respect to

Re: [gmx-users] density map in 3 Dimension

jagannath mondal wrote: Dear gromacs-users, I thought of sending this query again as I did not get any response in my last email. I was wondering whether there is any way to calculate the 3D density map of a particular selection of protein-water system ( say the water near the protein bac

[gmx-users] density map in 3 Dimension

Dear gromacs-users,  I thought of sending this query again as I did not get any response in my last email.   I was wondering whether there is any way to calculate the 3D density map of a particular selection of protein-water system ( say the water near the protein backbone) in gromacs. I guess g

[gmx-users] density of confined water

Hi,   I would like to know if there is a way in gromacs to calculate the time-averaged density of solvent which is confined between two objects , say, two plates or another example will be water confined between ligand and binding-pocket. I was thinking about two ways for going about this but in

Re: [gmx-users] density

Thanks Prof. Warren From: Dallas Warren To: Discussion list for GROMACS users Sent: Tuesday, November 22, 2011 12:23 AM Subject: RE: [gmx-users] density I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf –h”, method is

RE: [gmx-users] density

: Tuesday, 22 November 2011 4:28 AM To: Dallas Warren Subject: Re: [gmx-users] density Dear Prof. Warren Excuse me, may I know that how to obtain the average radial density functions relative to the center of mass with g_rdf? I think these plots are produced by counting the number of selected atoms

RE: [gmx-users] density

November 2011 5:52 PM To: gmx-users@gromacs.org Subject: [gmx-users] density Dear Prof. I have problems about density. I equilibrated my system consist 500 surfactants and 6 water molecules in martini coarse-grained for 120 ns and my results of g_energy next pr.mdp for density are: average

[gmx-users] density

Dear Prof. I have problems about density. I equilibrated my system consist 500 surfactants and 6 water molecules in martini coarse-grained for 120 ns and my results of g_energy next pr.mdp for density are: average = 907.701 err.est = 0.61 rmsd = 2.54989 tot-drift = -3.4173 I don't know a

Re: [gmx-users] Density

vferra...@units.it wrote: Dear all, I want to calculate the density of my system and visualize it during the simulation time. I've tried with g_density and with g_energy but in all the cases the density calculated is the average density all along the simulation and not the density of all th

[gmx-users] Density

Dear all, I want to calculate the density of my system and visualize it during the simulation time. I've tried with g_density and with g_energy but in all the cases the density calculated is the average density all along the simulation and not the density of all the system in each step of

Re: [gmx-users] density off

On 2011-04-20 20.10, Juliette N. wrote: Hi David, I used to apply NPT to fix the density, how can I get the denisty using NVT? You turn off P coupling and fix the right density by scaling using editconf. On 20 April 2011 13:46, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote: On

Re: [gmx-users] density off

Hi David, I used to apply NPT to fix the density, how can I get the denisty using NVT? On 20 April 2011 13:46, David van der Spoel wrote: > On 2011-04-20 19.40, Juliette N. wrote: > >> Hello, >> >> I am trying to obtain the density for my system that is exactly >> identical to experimental valu

Re: [gmx-users] density off

On 2011-04-20 19.40, Juliette N. wrote: Hello, I am trying to obtain the density for my system that is exactly identical to experimental value but whatever pressure I apply density is still off by 3%. Is this issue common? -- Thanks, Jennifer N. Yes, force fields are not perfect. How about run

[gmx-users] density off

Hello, I am trying to obtain the density for my system that is exactly identical to experimental value but whatever pressure I apply density is still off by 3%. Is this issue common? -- Thanks, Jennifer N. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listi

Re: [gmx-users] Density Differences

Ok Thanks. On Wed, Apr 13, 2011 at 6:22 PM, Justin A. Lemkul wrote: > > > Kavyashree M wrote: > >> The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983) >> stated a density of 0.999g/cc at 298K and 1atm, which is nowhere >> close to the value i have got. (1.025g/cc). or is this value

Re: [gmx-users] Density Differences

Kavyashree M wrote: The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983) stated a density of 0.999g/cc at 298K and 1atm, which is nowhere close to the value i have got. (1.025g/cc). or is this value tolerable? That's a 2.6% difference. I wouldn't call that "nowhere close." Unl

Re: [gmx-users] Density Differences

The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983) stated a density of 0.999g/cc at 298K and 1atm, which is nowhere close to the value i have got. (1.025g/cc). or is this value tolerable? On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul wrote: > > > Kavyashree M wrote: > >> I am

Re: [gmx-users] Density Differences

Kavyashree M wrote: I am sorry I did not include it in the mail: i used the following: pcoupl = Parrinello_Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p

Re: [gmx-users] Density Differences

I am sorry I did not include it in the mail: i used the following: pcoupl = Parrinello_Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 I agree that density of water is different depending on

Re: [gmx-users] Density Differences

Kavyashree M wrote: Dear gromacs users, I am trying to simulate a 225aa protein at 300K in water, with OPLSAA force filed, tip4p water model, using the parameters below (for pressure equilibration) during You're not doing NPT. You haven't specified pcoupl or any of the other relevant par

[gmx-users] Density Differences

Dear gromacs users, I am trying to simulate a 225aa protein at 300K in water, with OPLSAA force filed, tip4p water model, using the parameters below (for pressure equilibration) during position restrained md. integrator = md dt = 0.002 nsteps = 5

Re: [gmx-users] Density of methanol too low

On 2011-03-16 16.35, Jesús Carrete Montaña wrote: Dear list members, I am running some simple simulations of pure ethanol and methanol using the opls-aa force field as implemented in GROMACS 4.5.3, as a test case before attempting to study mixtures with more complex molecules. My problem is

[gmx-users] Density of methanol too low

Dear list members, I am running some simple simulations of pure ethanol and methanol using the opls-aa force field as implemented in GROMACS 4.5.3, as a test case before attempting to study mixtures with more complex molecules. My problem is that, even though there are published results [1] tha

Re: [gmx-users] Density of water, Dispcorr and rmsd

On 9/03/2011 10:43 PM, Kavyashree M wrote: Dear users, What is the difference between densities predicted by tip4p and spc models? I am using tip4p (with OPLSAA forcefield) in the simulation, during position restrained dynamics, Average water density is around 1015kg-m-3 at 300K which is

[gmx-users] Density of water, Dispcorr and rmsd

Dear users, What is the difference between densities predicted by tip4p and spc models? I am using tip4p (with OPLSAA forcefield) in the simulation, during position restrained dynamics, Average water density is around 1015kg-m-3 at 300K which is quite far from expt value.. The Dispersion

[gmx-users] Density of the box

Thank you Tsjerk! Actually I was not using any dummy atoms or united atoms in this case. I was using a pdb file with just water atoms (1BP2). Kindly excuse me I was not recieving any replys to my mail id ka...@rishi.serc.iisc.ernet.in. -- gmx-users mailing listgmx-users@gromacs.org http://li

Re: [gmx-users] Density of the box

Hi, editconf needs to take the masses from a database file if not fed with a run input file. It will probably miss out on some types of atoms or get the masses wrong, especially with united atoms and/or dummies. Probably the density would be correct giving a .tpr file for input. Cheers, Tsjerk

Re: [gmx-users] Density of the box

Sir, I am using Gromacs 4.0.7 version. Does this problem exits in other older or newer versions? what is the density of water that spc216 adds? If it is a fixed density, then i encountered a problem - I tried using 1 water molecule as a system (instead of protein), in a cubic box with 0.8nm

Re: [gmx-users] Density of the box

On 10/01/2011 7:59 PM, ka...@rishi.serc.iisc.ernet.in wrote: Dear Gromacs users, I was trying to run a simulation using a protein of 123 aa long and wanted to adjust the density to 993.04g/l so with the following command I ran the editconf: editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -den

[gmx-users] Density of the box

Dear Gromacs users, I was trying to run a simulation using a protein of 123 aa long and wanted to adjust the density to 993.04g/l so with the following command I ran the editconf: editconf -f conf.pdb -o box.pdb -bt cubic -d 0.8 -density 997.0479 Its output was as follows:

[gmx-users] Density question

Dear Gromacs Users, I run an MD simulation of a pure solvent and found out that the density of the solvent deviated a little bit from the actual experimental data. MD density is 880g/ml and the experimental data is 866g/ml. Is this reasonable for toluene solvent molecules. I have a hard

Re: [gmx-users] density tip3p

Hi Nisha,I did not try OPLSAA since I need TIP3P model with CHARMM. With this FF hydrogens are also considered as interaction sites. This is not very good combination for GROMACS, but it appeared that the differences are not too big and the time required for simulation with H interacttion side is s

Re: [gmx-users] density tip3p

Hi Zuzana, You are right. I did get my density to ~0.986g/cm3, and I actually came across this other paper by Price and Brooks, and initially they get a density of Tip3p using pme at around 0.979g/cm3, but they tweak some of the parameters in oplsaa to get the correct density. I am n

Re: [gmx-users] density tip3p

Hi Nisha,I have performed a benchmark simulations of TIP3P water and I still obtained density 0.984g.cm-3. It looks that this model gives such a density. If you look at JCP 79, 926, 1983 you will see that the authors got 0.982g.cm-3 with MC. (Table 3) Try to evaluate alsoo other properties, each mo

Re: [gmx-users] density tip3p

On 1/04/2010 4:58 AM, nishap.pa...@utoronto.ca wrote: Hello, So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS = integrator = sd tinit = 0 dt = 0.002 nsteps = 50 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0

Re: [gmx-users] density tip3p

Hello, So I looked at the manual and I changed my mdp parameters as follows to equilibrate at a constant pressure. RUN CONTROL PARAMETERS = integrator = sd tinit= 0 dt = 0.002 nsteps = 50 nstcomm

Re: [gmx-users] density tip3p

Thanks. I will look up the manual again. Quoting Sander Pronk : Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what

Re: [gmx-users] density tip3p

Hi Nisha, Looking at your .mdp, there are some issues that might lead to the behavior that you describe: First: you should try to look up the published densities for tip3p water at 300K - they might actually be close to what you get. Second: your neighbor list cut-off (rlist) might be too small

[gmx-users] density tip3p

I have a box (3x3x3nm) of Tip3p water molecules ~900 and the density when I create the box using genbox is 997.177g/l. I did energy minimization run and the potential energy did converge smoothly, so I did NPT equilibration run of 100ps and I got the density value of 975g/l. Why does the de

Re: [gmx-users] density vs time

nishap.pa...@utoronto.ca wrote: Near the end, the values are fluctuating around one. The reason I was That would seem right to me. trying to get density values was may be to try an understand if the density computed by gromacs is different for just water system and water+one methane sys

Re: [gmx-users] density vs time

I am trying to get an rdf graph actually, and my values are very close to one, but not exactly one, and I was wondering if there is some normalization issue with g_rdf? These are my values for rdf: 0 0 0.002 0 0.004 0 0.006 0 0.008

RE: [gmx-users] density vs time

hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of nishap.pa...@utoronto.ca > Sent: Wednesday, 17 March 2010 8:32 AM > To: gmx-users@gromacs.org > Subject: [gmx

Re: [gmx-users] density vs time

Justin A. Lemkul wrote: nishap.pa...@utoronto.ca wrote: Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e.

Re: [gmx-users] density vs time

nishap.pa...@utoronto.ca wrote: Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e. no pressure coupling. I tri

[gmx-users] density vs time

Hello, I am simulating one methane molecule in 899 water molecues in the box size of 3 3 3 nm (27nm^3). I would like to determine density vs time. Is there a way I can do that? I am running my simulation at constant Volume i.e. no pressure coupling. I tried using g_density but it give

RE: [gmx-users] density

> Date: Wed, 24 Feb 2010 14:46:17 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] density > > On 2/24/10 2:00 PM, Sander Pronk wrote: > > You got pretty close to what the density of SPC water is at 298K > > > > Acc

Re: [gmx-users] density

On 2/24/10 2:00 PM, Sander Pronk wrote: You got pretty close to what the density of SPC water is at 298K According to "Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density", William L. Jorgensen, Corky Jenson, J. Comp. Ch

Re: [gmx-users] density

You got pretty close to what the density of SPC water is at 298K According to "Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density", William L. Jorgensen, Corky Jenson, J. Comp. Chem, Volume 19 Issue 10, Pages 1179 - 118

Re: [gmx-users] density

On 2/24/10 1:23 PM, Sunil Thapa wrote: Respectable Experts Grettings I am studying diffusion of an oxygen molecule in 255 molecule of SPC water. I need to determine diffusion coefficient at temperature 298 K and 1 atm pressure. In order to do that using editconf I scaled the density of the system

[gmx-users] density

Respectable Experts Grettings I am studying diffusion of an oxygen molecule in 255 molecule of SPC water. I need to determine diffusion coefficient at temperature 298 K and 1 atm pressure. In order to do that using editconf I scaled the density of the system including oxygen to 1g/l. I checked t

[gmx-users] density problems when switching from md to sd integrator

Dear Aymeric: 1. Can we please see the entire .mdp files for both simulations? I suggest that you use a tau_t=1.0 (0.2 is probably over-damped). 2. Although any value of tau_t should still produce the correct equilibria, your diffusion rates and your overall sampling may be slower with sd

[gmx-users] density problems when switching from md to sd integrator

Dear users, I'm simulating a box of cyclohexane (GROMOS 53a6, 512 molecules, 298K, compressibility=11.2 10-5 bar-,1 tau_p=0.5 ps, no constraints on bonds). After equilibration and NPT simulation, the system reaches the proper density reported for the model (791g/L). When I switch to a stochast

Re: [gmx-users] Density

Carla Jamous wrote: Thank you Mark, for your answer. This time I have another issue: temperature. What are the ways to control temperature in gromacs (during heating or equilibration phases), other than temperature coupling? I don't see how that's even possible. By definition, temperature

Re: [gmx-users] Density

Thank you Mark, for your answer. This time I have another issue: temperature. What are the ways to control temperature in gromacs (during heating or equilibration phases), other than temperature coupling? Thank you Carla On Thu, Jan 14, 2010 at 10:40 PM, Mark Abraham wrote: > Carla Jamous wrote:

Re: [gmx-users] Density

Carla Jamous wrote: Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. Those tools report density-related quantities, they do not control it. However, when I use g_energy, in my list, "Density" doesn't appear.

Re: [gmx-users] Density

Carla Jamous skrev: Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. However, when I use g_energy, in my list, "Density" doesn't appear. Else, if I use g_density, it needs a file traj.xtc which I don't have. S

[gmx-users] Density

Hello, I'm experiencing some difficulties with gromacs. In order to control my system's density, I have to use g_energy or g_density. However, when I use g_energy, in my list, "Density" doesn't appear. Else, if I use g_density, it needs a file traj.xtc which I don't have. So please can anyone tell

[gmx-users] Density Profile

Hi, I obtained the electron density profile for the solvent in protein membrane simulation, For this I used the following commands: ]$ g_density -f md.xtc -s md.tpr -d z -dens electron -o sol.xvg -ei electrons.dat -symm -n index.ndx Although in md.gro file is seen any water in m

Re: [gmx-users] Density histogram in Ramachandran plot

Here in the gromacs user contribution: http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software I use it once. Anthony On Thu, Nov 12, 2009 at 7:49 PM, Mark Abraham wrote: > ms wrote: >> >> Hi, >> >> I wonder if there is an easy way I am missing to get

Re: [gmx-users] Density histogram in Ramachandran plot

ms wrote: Hi, I wonder if there is an easy way I am missing to get a density histogram from the Ramachandran plot over a trajectory as outputted by g_rama. All I see are big, uniform black blobs and they're not helpful, because with tons of data points a density plot would be much more informati

[gmx-users] Density histogram in Ramachandran plot

Hi, I wonder if there is an easy way I am missing to get a density histogram from the Ramachandran plot over a trajectory as outputted by g_rama. All I see are big, uniform black blobs and they're not helpful, because with tons of data points a density plot would be much more informative. Thanks!

Re: [gmx-users] density and intramolecular interactions

Alexey Odinokov wrote: Hi everyone, I have a model for liquid benzene. In this model all bonds are treated as harmonic potentials. When I use larger constants for these potentials (to make molecules more planar), the average density of my benzene (from NPT ensemble) becomes lower. Does virial dep

[gmx-users] density and intramolecular interactions

Hi everyone, I have a model for liquid benzene. In this model all bonds are treated as harmonic potentials. When I use larger constants for these potentials (to make molecules more planar), the average density of my benzene (from NPT ensemble) becomes lower. Does virial depend on intramolecular int

Re: [gmx-users] Density Problem

The water box is about 10nm in z direction. x and y box sizes are about 3.3nm. Hui On Fri, Apr 24, 2009 at 7:17 PM, Mark Abraham wrote: > Zhang Hui wrote: > >> Dear All, >> >> I just found that there is a problem when I extract the density >> of water from my Gromacs simulations. >> >>

Re: [gmx-users] Density Problem

Zhang Hui wrote: Dear All, I just found that there is a problem when I extract the density of water from my Gromacs simulations. When I used g_density to get the water density from .trr trajectory file, the density plot looked normal. But when I used trjconv to convert the .tr

[gmx-users] Density Problem

Dear All, I just found that there is a problem when I extract the density of water from my Gromacs simulations. When I used g_density to get the water density from .trr trajectory file, the density plot looked normal. But when I used trjconv to convert the .trr to .gro file, and

[gmx-users] Density Problem

Dear All, I just found that there is a problem when I extract the density of water from my Gromacs simulations. When I used g_density to get the water density from .trr trajectory file, the density plot looked normal. But when I used trjconv to convert the .trr to .gro file, and

RE: [gmx-users] density around protein

Or g_sdf Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is

Re: [gmx-users] density around protein

g_sorient returns the number of solvent molecules within a given distance range of a protein -- it may be what you are looking for. Matt 2009/4/5 Morteza Khabiri : > Dear gmxusers > > I want to calculate the density of solvent around protein. > I already tried the commands g_density and g_densmap

[gmx-users] density around protein

Dear gmxusers I want to calculate the density of solvent around protein. I already tried the commands g_density and g_densmap but the results are not the the things that I want. The g_density Compute partial densities across the box and g_densmap just give me one black and white photo which don't

Re: [gmx-users] density of the bilayer

On 12 Nov 2008 11:41:54 - "minnale " <[EMAIL PROTECTED]> wrote: Thanks for your reply, In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it incr

Re: Re: [gmx-users] density of the bilayer

Thanks for your reply, In case of water density, starting of the water density will be for some time should come straight line in the graph later gradually reducing and goes to zero towards centre of the bilayer again it increases and stop going the water density. but in my case starting wa

Re: [gmx-users] density of the bilayer

On 12 Nov 2008 11:13:51 - "minnale " <[EMAIL PROTECTED]> wrote: Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc i

[gmx-users] density of the bilayer

Hi users, Intially I have run the simulation of the bilayer for 5ns then extended this to 20ns. When analyse density of the bilayer by considering trajectories of these different timings one at 5ns.xtc anonther at 20ns.xtc its showing almost same density values how come it is possible? the

Re: [gmx-users] density graph ( density vs time)

g_energy output gives the x-axis as time... -Justin thanks --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: From: Justin A. Lemkul <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: [EMAIL PROTECTED], "Discussion list for GROM

Re: [gmx-users] density graph ( density vs time)

gt; --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > >> From: Justin A. Lemkul <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] density graph ( density vs time) >> To: [EMAIL PROTECTED], "Discussion list for GROMACS users" >> >&g

Re: [gmx-users] density graph ( density vs time)

I used g_energy before but i just obtained density (y-axis) versus box length (x axis). now i wish to obtain density vs time thanks --- On Tue, 10/28/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] densi

Re: [gmx-users] density graph ( density vs time)

, 10/28/08, Mark Abraham <[EMAIL PROTECTED]> wrote: From: Mark Abraham <[EMAIL PROTECTED]> Subject: Re: [gmx-users] density graph ( density vs time) To: "Discussion list for GROMACS users" Date: Tuesday, October 28, 2008, 4:46 PM huan wrote: Dear all gmx-users and deve

Re: [gmx-users] density graph ( density vs time)

TED]> wrote: > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] density graph ( density vs time) > To: "Discussion list for GROMACS users" > Date: Tuesday, October 28, 2008, 4:46 PM > huan wrote: > > Dear all gmx-users and developers.

Re: [gmx-users] density graph ( density vs time)

huan wrote: > Dear all gmx-users and developers. > > I wish to get a density graph with density versus time instead of nm, so how > can i obtained this? You could extract the box vectors with g_energy and compute the density from the volume. Best, Jochen > > Thanks. > > > > > _

Re: [gmx-users] density graph ( density vs time)

huan wrote: Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Please ask a more specific question. We can't tell whether your problem is knowing what tool to use, how to use it, how to label axes of plots

[gmx-users] density graph ( density vs time)

Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] density graph 2

Dear all Gmx users and developers, How can i get a density graph with x-axis is time scale? I obtained a density graph using g_density which output a graph with density vs nm (box size). So how can i get a graph with density vs time? Thanks _

Re: [gmx-users] density graph

Thanks Justin, I realized my mistake. I get the kj/mol unit because i use g_energy command and select the density option. thanks --- On Wed, 10/15/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users]

Re: [gmx-users] density graph

huan wrote: Dear all gmx users and developers, Is it correct that in gromacs energy (density graph), the y-axis is labelledas kJ/mol, I am wonder it is not a density unit. In the output that I have from g_density (v 3.3), the the .xvg file has the y-axis labeled as: yaxis label

[gmx-users] density graph

Dear all gmx users and developers, Is it correct that in gromacs energy (density graph), the y-axis is labelled as kJ/mol, I am wonder it is not a density unit. Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o

Re: [gmx-users] density and CG MARTINI force field

merc mertens wrote: Dear people, I am trying to use the MARTINI CG force field from Marrink et al. for a 100 residue protein in water. I use the tools from the Marrink website (http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the necessary gro and itp files. For solva

[gmx-users] density and CG MARTINI force field

Dear people, I am trying to use the MARTINI CG force field from Marrink et al. for a 100 residue protein in water. I use the tools from the Marrink website (http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the necessary gro and itp files. For solvation of my protein I u

Re: [gmx-users] density calculation of genbox

Mark, thank you for reply! In the output file of genbox the 'right' box size is written: 8.8 8.8 8.8 Tobias On Fri, 7 Mar 2008, Mark Abraham wrote: Tobias Unruh wrote: Hi, I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane (C32H66) molecules (molecular w

Re: [gmx-users] density calculation of genbox

Tobias Unruh wrote: Hi, I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane (C32H66) molecules (molecular weight: 450.88 g/mol). This gives a density of 793.23 g/l. But genbox calculates 743.576 g/l. The atom masses and numbers of atoms are ok in the input .gro file. Some su

[gmx-users] density calculation of genbox

Hi, I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane (C32H66) molecules (molecular weight: 450.88 g/mol). This gives a density of 793.23 g/l. But genbox calculates 743.576 g/l. The atom masses and numbers of atoms are ok in the input .gro file. Some suggestions? Best rega

Re: [gmx-users] Density Deferences between spc216 and tip4p water models

[EMAIL PROTECTED] wrote: Dear All, I was trying create a box (cubic 10 10 10) of water. I am a bit surprised by looking at the density deferences between spc216 and tip4p water models. I am giving the brief output below. genbox -cs tip4p.gro -box 10 10 10 Output configuration contains 131540

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