[gmx-users] Topology and force fields

Hello all, Below are the contents of a water1.top file that I used to simulate 2000 molecules of TIP3P water (NPT). I made this topology file according to the pattern on page 114 of the manual (topology for Urea in water). My diffusion coefficient, viscosity and radial distribution functi

[gmx-users] Re: Parameters for AOT molecule/Too few parameters on line

502080.0 CACA10.1375255224.0 CE1CE110.134368192.0 CE1CE210.1342418400.0 CE1CT210.1502305432.0 Thank you, Lum > Lum Nforbi wrote: > > Hello all, > > > > I have built a parameter file for the AOT surfactant mole

[gmx-users] Parameters for AOT molecule/Too few parameters on line

Hello all, I have built a parameter file for the AOT surfactant molecule and tried to minimize the energy of a mixture of several of this molecule and water molecules but I have the warnings at the bottom part of this mail. Gromacs basically goes through all the lines of parameters starting fr

[gmx-users] X's in the ffcharmm27bon.itp force field

Hello all, Please, can someone let me know why there are X's in the [dihedraltypes] section of the ffcharmm27bon.itp force field and what they actually stand for? Could they be replaced with actual atoms or no? I appreciate your replies. Lum -- gmx-users mailing listgmx-users@gromacs.org h

[gmx-users] Re: How to include sodium ion (Reply to Justin's mail)

use gmail and when I click the reply tab, it includes all the mails for that issue, and there is no "subject" entry. So I always have to copy and paste the mail before replying. I appreciate your help). Lum Nforbi wrote: > Hi All, > >I would like to include sodium ions in

[gmx-users] How to include sodium ion

Hi All, I would like to include sodium ions into a water/AOT (sodium di-2-ethylhexylsulfoccinate) cubic box. Can someone tell me how to do this and how to include parameters for the sodium ion in the parameter file? I appreciate your answers. Lum -- gmx-users mailing listgmx-users@gromacs

[gmx-users] Re: Choice of value of rlist, rvdw and rcoulomb

Dear Mark and Amit, I appreciate your replies. I have read this portion of the gromacs manual which talks about cut-offs, but I don't clearly understand the physical significance of the choice of values. I am using for my experiments vdwtype = cutoff, which is twin-range cut-off with rlist =

[gmx-users] Choice of value of rlist, rvdw and rcoulomb

Hi all, Please, can someone let me know if the choice of the value of rlist, rvdw and rcoulomb is related to or depends in someway to the distance between atoms on a lennard-jones potential plot? I appreciate your answers. Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gr

[gmx-users] Cut-offs in gromacs

Dear all, I did two md simulations of 200 particles each of a lennard-jones fluid. One of them gave me the correct pair distribution function for a lennard-jones fluid (converging to 1) and one did not (converging to zero). I have attached the .mdp files for both systems below. The barosta

Re: [gmx-users] Restarting mdrun

Hi Chadan, I have used the two commands below to CONTINUE a run and they worked fine for me. I am also using gromacs-4.0.5. tpbconv -s wfullmdrun_extend2.tpr -extend 2000 -o wfullmdrun_extend3.tpr mdrun -s wfullmdrun_extend3.tpr -o wfullmdrun_traj.trr -e wfullmdrun_ener.edr -g md.log -cpi sta

[gmx-users] Working with Reduced Units

Hi all, Please, can someone shed more light on how to set up reduced units in an .mdp file? I have tried to this but it does not work. I set epsilon, sigma and mass to 1 in my force field file as stated in section 2.3 of the manual. I multiplied 300K temperature by 0.00831451 and divided by

[gmx-users] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.

Hello all, After minimizing the energy of my system of 200 particle coordinates of box dimension 3.5 nm to an acceptable value, I proceeded to doing mdrun but got the error message: "Source code file: nsgrid.c, line: 348. Fatal error: Number of grid cells is zero. Probably the system and box

[gmx-users] Re: Lennard-Jones Rdf plot

ards. In section 2.3 of page 9 of the manual, it is mentioned that reduced units are good for simulating LJ systems, but Gromacs already has a fixed set units that it uses and I am not sure how to set the reduced units such that Gromacs can recognize them. Could it be a reduced units problem? I appre

[gmx-users] Lennard-Jones Rdf plot

Dear all, Please, could someone tell me what could be the problem with the attached LJ plot? Could it be due to wrong assignment of periodic boundary conditions? Thank you, Lum RDF_oxyxoy Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

[gmx-users] Genbox error message

Hello all, Can someone tell me the meaning of this error message after using the genbox command? *** glibc detected *** genbox: munmap_chunk(): invalid pointer: 0x095969c8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7e7c454] genbox[0x81195c4] === Memory map: 0804

[gmx-users] Gromacs 4.1

Hi Mark, When will Gromacs 4.1 be available? Thank you, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list.

[gmx-users] Simulation with Implicit solvents

Hello all, Has anyone done simulation with implicit solvents? If so, please, could you let me know how implicit solvents are set up, in general? Is there some documentation where I could find this information in? Thank you, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.

[gmx-users] Re: Opening .o files - in response to Erik's question.

ad an easier-to-understand code and that's why I tried opening the g_energy.o file. This may be dumb but I am not quite used to the files and I will eventually get it. If the gmx_energy.c file is the source code, is there a way convert it into, for example, fortran? Thank you, Lum > Lum

[gmx-users] Opening .o files

Dear all, I am having problems opening the g_energy.o file in the gromacs-4.0.5 folder. Can someone tell me how to open this file? What is the general way of opening .o files? Thank you, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Viscosity determination

Dear all, Below is my output for viscosity determination. In order to get a value for the viscosity, do I just take an average of the numbers in the third column? # This file was created Wed Jan 6 16:25:24 2010 # by the following command: # g_energy -f wfullmdrun_ener.edr -vis viscosity.xvg #

Re: [gmx-users] Problems with calculating Cv and Cp

__ > ___ > Andrew Paluch > Department of Chemical and Biomolecular Engineering > University of Notre Dame du Lac > apal...@nd.edu > ___ > __

[gmx-users] Calculation of Cp

Dear All, I have been struggling with this for over a month now and I have still not been able to figure out how to calculate the Cp of my system of 2000 molecules of water on which I did an NPT simulation. The g_energy command of my system gives a wrong Cv (~12.4749 J/mol.K), which therefore

[gmx-users] Fwd: What could be wrong with rdf plot?

-- Forwarded message -- From: Lum Nforbi Date: Thu, Dec 31, 2009 at 12:33 PM Subject: What could be wrong with rdf plot? To: gmx-users@gromacs.org Dear all, I am currently analyzing a system of 2000 molecules of TIP3P water on which I performed a NPT simulation. The plot

[gmx-users] Using GENCONF

Hi all, Is there a way to use genconf such that it does not reproduce the exact same coordinates over and over again (or multiples of the same coordinates) but assigns different coordinate values to each atom in the x, y and z directions? Thanks, Lum -- gmx-users mailing listgmx-users@grom

[gmx-users] Problems with calculating Cv and Cp

Dear all, I have run an 8 ns NPT simulation of 2000 molecules of TIP3P water and I have a very low Cv value of 12.4748 J/mol K (factor = 0.000164481). The result is below. I ignored this value and have tried using formulas for Cv that I found in the two books: Allen and Tildesley & J. M. Ha

[gmx-users] Re: RDF plot. This is weird!

Hi Justin, I chose my whole system of 2000 water molecules. I discussed this plot with someone and they said that rdf can be plotted for atoms as well as whole molecules and that the shape of my rdf plot was not a problem of my having used the whole system (I am not really sure about this). T

[gmx-users] Fwd: RDF plot. This is weird!

Hi, I am forwarding the message and the attachment because I did not see my message in the inbox of gmx-users; I saw only the attached file. Please, can the text be included? Thank you. -- Forwarded message -- From: Lum Nforbi Date: Wed, Dec 9, 2009 at 11:59 AM Subject: RDF plot

[gmx-users] RDF plot. This is weird!

Dear all, I have attached a RDF plot of 2000 molecules of water (SOL is the system name). It does not follow the normal trend. I used the command line below to get this plot: g_rdf -f wfullmdrun_traj.xtc -s wfullmdrun_extend3.tpr -o wfullmdrun_rdf.xvg The run took about 1h 45 min to be complete.

[gmx-users] To continue a run

Hello all, I am a little confused with this. Which of these 2 files is used when continuing a run: state.cpt or state_prev.cpt? These are binary files. Is there a way to view them? Thank you, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

[gmx-users] Radial distribution specifications

Dear all, I need to plot the radial distribution functions but I am not sure how you specified the different radial pair distribution functions for H2O: gOO, gOH and gHH, in order to have different plots. Please, can you help me out with this? Thank you, Lum -- gmx-users mailing listgmx-use

[gmx-users] How to plot Pressure (bar) vs simulation time in ps

Hi everyone, I need to plot a graph of pressure (bar) vs run time (ps) but I am havin problems with this because the graph's y-axis diplays energy (KJmol^-1) instead of pressure. How can I correct this energy on the y-axiz of my plot to pressure (bar)? I have used this command to view the value o

[gmx-users] Genbox

Hello all, How long does it usually take genbox to run? Thanks, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to th

[gmx-users] RE:How to check for bad contacts.

Hello Dr. Warren, Thank you for the useful information. I did use vmd to view my molecule, but in a system of 2000 molecules, it is quite difficult to locate atom 2065 (an O atom) which is actually the offending atom. I have described the way I did the work below. I used a random generator softwar

[gmx-users] How to check for bad contacts

Hello, How do you check for bad contacts in a system that cannot be minimized? Thanks, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subsc

[gmx-users] Calculating density of a particular run segment

Hello all, I have tried this command line to find the density of a system at particular time interval: g_density -f traj.xtc -s topol.tpr -b 1228 -e 1328 -o density.xvg, but I keep having the result to the full mdrun. The plot of the density vs box dimension is also obtained via xmgrace. I ne

[gmx-users] Problem with system minimization

Hello all, I am minimizing a system of 2000 water molecules again but I have several error messages. Is my timestep too large indeed? The error message also mentions segmentation fault. I have only 6000 atoms in my system but the output shows atom 7783 and 8879. I'm not sure what's going on. My pd

[gmx-users] Determination of heat capacity of water at constant pressure

Dear All, Can someone give me an explanation of how to calculate the heat capacity of water at constant pressure after completion of the mdrun? Thank you, Lum ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/list

[gmx-users] grompp output on terminal

Hello everyone, I had written earlier today about my concern involving grompp. I am trying to minimize the energy of a pure water system using grompp: grompp -f waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr and part of the output on the terminal is as follows: Analysing resid

[gmx-users] Opening aminoacids.dat file during grommp

Hello all, I am running grommp which kind of goes "successfully" but I am a little concerned about the fact that one of the messages in the terminal says "opening aminoacids.dat file" and in another message says "OTHER: 2000 residues found." I guess this 2000 is refering to the 2000 water molecul

[gmx-users] Error message: Cut-off length is longer than half the shortest box vector

Hello everyone, Thanks to Tsjerk, Mark Abraham, Justin and Dr. Vitaly for the very useful inputs to my quest for generating a .gro file from a .pdb file. I am now trying to minimize the energy of the system so I can do an mdrun but I keep having the error message: the cut-off length is

[gmx-users] Generating a .gro file from .pdb file

Hello everyone, Thanks to Justin Lemkul and Thomas Schlesier for replying to my question in vol. 65 issues 96 and 98. I am trying to convert a pdb file to a gro file using pdb2gmx -f waters.pdb -o waters.gro and I get the message: Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMO