[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 Please

[gmx-users] Re-compile Gromacs Program?

Hi I found the Gromacs Program could not do the parallel computing since the staff of the compter center in my school upgraded the intel compiler to v 12, and rebuilt the mpich build with intel. I requested them to recompile the Gromacs Program but they rejected and they answered that the updated i

[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

Hi I want to protein's domain motion. I use g_covarandg_anaeig to get the eigenvectors. How can i get the rotational axis of which protein do its domain motion from those eigenvectors? I found the papers and the authors plot its rotational axis of domain motion. How did they make it ?

[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

Message: 1 Date: Thu, 26 May 2011 19:54:29 -0700 From: Chih-Ying Lin Subject: [gmx-users] Domain Motion => How do get the rotational axis fromeigenvectors ? To: gmx-users@gromacs.org Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi I want to protein'

[gmx-users] How to calculate RMSD per residue with Gromacs ?

Hi How to calculate RMSD per residue with Gromacs ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscrib

[gmx-users] Counting number of non-bonded interactions ?

Hi Is there any function to count number of non-bonded interactions with Gromacs ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

[gmx-users] Counting non-bonding interaction

Hi Is there any function counting non-bonding interaction with Gromacs ? Thanks Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't

[gmx-users] Is Gromos force field 45a3 out of dated?

Hello, I submitted a paper and get rejected immediately by editor because of the following comment. "The simulations described here rely on an outdated force field (Gromos 45a3) and I suspect that the partial unfolding described here is at least in part due to force field artifacts. " Our simula

[gmx-users] Re: Questions

Hi Tsjerk: I still have questions here. 1. Although you have explained the differece between HOH, AHOH and BHOH, I do not fully understand. => Can I delete all of atoms, HOH, AHOH and BHOH ? 2. So, in your tutorial, you use "united atom" algorithm, right? and, "pdb2gmx" can recognize the "uni

[gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

Hi GROMOS 45a3 force field GROMOS 53a6 force field Are they compatible? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

[gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

Hi GROMOS 45a3 force field GROMOS 53a6 force field Are they compatible? I notice that MOST of the force field parameters sets are THE SAME in the GROMOS 45a3 and GROMOS 53a6. So, I want to ask if GROMOS 53a6 is rectification from GROMOS 45a3. I mean if GROMOS 53a6 match more experimental data th

[gmx-users] Protein-Ligand Docking?

HI When i visualize the MD trajectory, the protein and ligand are closed by. But, I don't know if ligand really DOCK on the protein. Please tell me how to define the successful docking. Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] Protein-Ligand Docking?

HI Would you please give me an example of "definition" of DOCKed? Thank you Lin First step, define what you mean by being "DOCKed". Second step, determine if those conditions are meet by your protein and ligand. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology an

[gmx-users] Protein-Ligand Docking?

een given the protein and the surfactant and tried to "see" if the surfactant will dock on the protein. => what is the next step that I can do? Thank you very much Lin Chih-Ying Lin wrote: > HI > Would you please give me an example of "definition" of DOCKed? > Y

[gmx-users] how to make the different displacement of ligand around protein?

Hi how to make the different and specific displacement of ligand around protein with GROMACS? i only know how to make the ligand randomly displaced around protein. Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org

[gmx-users] how can i know the center of the cleft of protein?

Hi how can i know the center of the cleft of protein? I mean how to calculate or use Gromacs to know the center (x,y,z) of the cleft of protein? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] how to setup the pH value

Hi How to set up the pH value ? what ions should I put in the solution? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

[gmx-users] Segmentation fault

Hi I run the simulation on MPI. first, i make constraints=all bond => successful second, i make constraints=none => segmentation fault is the "segmentation fault" coming from the NONE bond-contraints? Thanks Lin ___ gmx-users mailing listgmx-u

[gmx-users] How can i know if the protein swell during the MD simulation?

HI How can i know if the protein swell during the MD simulation? What are those indications to "see" the swollen protein? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search t

[gmx-users] dt > = 0.002

Hi I want to get the simulation results fater and want to set the time step dt > = 0.002 what is the upper limit of the time step dt ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-user

[gmx-users] What is the purpose that we make the bond constraints?

Hi All atoms are connected by the covalent bonds and all atoms are constrainted by the force field. Why do we need the bond constraints? What is the purpose that we make the bond constraints? I read the manual but could not answer the question by myself. How do the following parameters work? ; O

[gmx-users] Why does protein carry charges?

Hi I got the protein crystal structures from the PDB file. There are only residues and water in the PDB files. Why does the protein carry charges? Why aren't they electrically neutral? What are their intrinsic counter ions ? Thank you Lin ___ gmx-users

[gmx-users] How to choose the counter ions for proteins?

Hi How to choose the counter ions for proteins? Proteins are made of amino acids. Does it mean the counter ions of protein H+ or OH-? I think => H+ and OH- ions are not available for the gromos force field, right? But, later version 4.0.2 ; they might be available, right? Thank you Lin __

[gmx-users] Why NaCl and KCl solution?

HI 1. Would you please tell me the reason that "generally people use NaCl or KCl in the solution with protein"? 2. Why does PDB file of the protein NOT Carrying ions? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gro

[gmx-users] The default pH =7.0 ???

Hi Does the Gromacs set the default pH = 7.0 ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

[gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx

Hi after the command pdb2gmx, the protein will be added appropriate H, So, does pdb2gmx add H (protonate) based on pH =7.0 ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please searc

[gmx-users] Counter ions added

Hi I search some papers based on MD. Most of them did not tell what the counter ions they added. Why? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:/

[gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx

is this command => pdb2gmx -f 1LW9.pdb -o 1LW9.gro -p 1LW9.top at what condition Gromacs calculate the charges of the protein?? Thank you Lin Chih-Ying Lin wrote: > Hi > after the command pdb2gmx, > the protein will be added appropriate H, > > So, does pdb2gmx add H (p

[gmx-users] The system setup

Hi I am going to simulate the lysozyme with some ligand in the low ionic strength phosphate buffer . The buffer condition will be (pH 7.2, 8.3 mM) and (pH 5.0 , 8.3 mM) For the buffer condition (pH 7.2, 8.3 mM), I will use TIP3P water model and use CL- ions to nutralize the lysozyme (+8) and c

[gmx-users] protein molecular weight?

Hi : Would anyone explain how to get the protein molecular weight from the following note from the catalog? mol wt single-chain mol wt 14.7 kDa What does it mean single-chain? Is it correct => 1 kDa = 1000 Da = MW 1000. So MW 240 = 0.24 kDa. Thank you Lin _

[gmx-users] protein molecular weight?

hicken egg white lyophilized powder, protein ... http://www.sigmaaldrich.com/catalog/ProductDetail.do?N4=L7651%7CSIGMA&N5=SEARCH_CONCAT_PNO%7CBRAND_KEY&F=SPEC Thank you Lin Chih-Ying Lin wrote: > Hi : > Would anyone explain how to get the protein molecular weight from the >

[gmx-users] How to print out .gro per 100 ps?

Hi I want to simulate the system straight to 1ns. How to print out .gro per 100 ps? I only know Gromacs can print out the .gro file at the end of the simulation. How can I print out the .gro in the middle way of simulation? Thank you Lin ___ gmx-users

[gmx-users] g_energy returns the instantaneous data or the average data?

Hi I want to calculate the pressure and the energy for the system. my .mdp file is as follows; writing out the energy and coordinates per 1000 steps. nstenergy = 1000 ; Writing out energy information every step nstxtcout = 1000 ; Writing coordinates every step After entering g_energy comman

[gmx-users] Final Temp = 303 K ?

Hi I was running the MD simulation and you the Berendsen method. Here is my .mdp file. ; Temperature coupling Tcoupl = Berendsen tc-grps = Protein Non-Protein tau_t= 0.1 0.1 ref_t= 300 300 But the final Temp =

[gmx-users] g_energy

Hi I have read the manual , Appendix C. After the command g_energy => Energy Average RMSD Fluct. Drift Tot-Drift --- Potential -196428372.215340.8525.1803

[gmx-users] Final Temp = 303 K ?

Hi Here is my whole md.mdp. But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? The simulation system is protein + ligand + counter ions. ligand is the 33-atom molecule. force field ffG45a3.

[gmx-users] g_energy => both instantaneous and average

Hi I have read throught the Appendix C. The following is the .mdp file. Type the command g_energy -f abc-NVT500.edr -o abc-NVT500.xvg choose Pressure Based on my understanding of the Appendix C => g_energy will print out the instantaneous Pressure every 1000 step and save it into abc-NVT500.xv

[gmx-users] coulombtype = Reaction-Field => heat up the system

Hi I set up Tcoupl = Berendsen. ref_t = 300 K the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? the final Temp = 303 K and stable. Can I analyze the data from this simulation? The simulation

[gmx-users] g_energy => RMSD = Standard Deviation?

HI After the command g_energy => the value of RMSD is shown, I can not find the math definition of RMSD from manual. Is the math definition of RMSD = Standard Deviation in Statistics? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] trjconv -pbc -center

Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I supposed that the ligands dock/attach on the protein. I want to center the protein and see if the ligands dock/attach on the protei

[gmx-users] trjconv -pbc atom -center rect

Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. with this command => trjconv -pbc atom -center rect the most part of the protein is still in the right edge of the box the small par

[gmx-users] The Cut-off for coulombtype heat up the water system?

Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 1. From Berk => use multiple groups. => how ??? => I have been thinking that it is better to group the molecule => such as: protein , non-protein 2. change the coulombtype without th

[gmx-users] g_energy => RMSD vs Fluctuation

Hi The definition of the Fluctuation is shown on the Manual, Appendix C, eqn (C.1) The definition of the RMSD is as shown from the link. http://en.wikipedia.org/wiki/Root_mean_square_deviation The definition of the estimators is unclear though. So, what is the definition of the estimators? The fo

[gmx-users] trjconv -pbc nojump -center rect => does not work

Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I am very sure that the ligand has attached to the protein. with this command => trjconv -pbc nojump -center rect so, ho

[gmx-users] g_energy => the reasonable range of RMSD or Fluctuation ?

HI Once the system reaches the equilibrium, the thermal properties still fluctuate within some range. What is the reasonable/trustable range of RMSD or Fluctuation of those thermal properties ? Thank you Lin ___ gmx-users mailing listgmx-users@grom

[gmx-users] g_coord => command not found

Hi g_coord is introduced in the Chapter 8 of the Manual. But, when I typed g_coord -h => command not found. What is the NEW name of the g_coord? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

[gmx-users] What is the important thing when we are watching the MD trajectory movie?

Hi What is the important thing when we are watching the MD trajectory movie? Are people watching the whole trajectory movie? It might take 3-4 hours or longer. What is the efficient way to watch the trajectory movie? Thank you Lin ___ gmx-users mailing

[gmx-users] install DSSP ???

Hi I want to install DSSP in my mac, tiger. I have searched the procedure of installing DSSP but still cannot install it sucessfully. 1. I go to this website http://swift.cmbi.kun.nl/gv/dssp/ to install the source codes and the Linux executable file "dsspcmbi". I put both the source codes and t

[gmx-users] Install DSSP=> cannot execute binary file ???

1. I go to this website http://swift.cmbi.kun.nl/gv/dssp/ to install the source codes and the Linux executable file "dsspcmbi". I put both the source codes and the executable file "dsspcmbi" in the same document. 2. follow the procedures in the website http://biskit.pasteur.fr/install/applicatio

[gmx-users] What much time does DSSP need to analyze lysozyme?

Hi 1. After compiling, the two following files are created. dsspcmbi dsspcmbi.exe 2. The path of the DSSP file is /usr/local/bin/DSSP. Both dsspcmbi and dsspcmbi.exe are in the file /usr/local/bin/DSSP. 3. So, the last step i type the command in my .profile. setenv dssp /usr/local/bin/DSSP

[gmx-users] How much does DSSP need to analyze lysozyme? => more than one hour

HI 1. type => do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg Select a group: 1 Selected 1: 'Protein' There are 129 residues in your selected group Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Bac

[gmx-users] How can i make the DSSP picture like picture 8.10 in the Maunual ?

Hi I have installed DSSP and GIMP. Also I have done some cases with DSSP and GIMP. With GIMP, I did not get the coordinates written as residues vs time(ps). I also did not get the bottom bar in the picture 8.10 in the Manual. Coil Bend Turn A-Helix B-Bridge How can I make the DSSP picture like

[gmx-users] g_energy=> Different Average values?

Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. Energy Average RMSD Fluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711 -63.5543 Kinetic En. 51901.5 259.034 259.015 -0.02151 -10.7574 Total Energy -215421 275.52 274.683 -0.148

[gmx-users] .mdp => Dihedral Angles conflict Bond Constraints ?

Hi In the .mdp file, i set lincs-warnangle = 30. Will the dihedral angles be affected? Will the maximum, possible values of the dihedral angles be reduced because of the setup of the bond constraints? Thank you Lin ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs un

[gmx-users] .mdp => Dihedral Angles conflict Bond Constraints ?

30 this allows each covalent bond to rotate at most 30 degrees all bonds have less degree of freedom to rotate.. So, I think the dihedral angle will be affect... and the dihedral angle will some or less decreased. ?? Thank you Lin On Jul 6, 2009, at 20:58, Chih-Ying Lin wr

[gmx-users] Competition of electric force and hydrophobicity

Hi Is there any idea about the competition of electric force and hydrophobicity ? thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

[gmx-users] g_energy=> Different Average values?

Hi I have read through the manual but could not get it. Would you please explain it more? Thank you Lin Chih-Ying Lin wrote: > > > Hi > After the command, > g_energy -f abc.edr -o abc.xvg > > the average values is printed out on the screen. > Energy > Av

[gmx-users] Where are the source codes?

Hi I have installed the Gromacs and I want to see the source codes. Which directory can I find them? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http:

[gmx-users] about template.c?

Hi inside template.c => #include "statutil.h" #include "typedefs.h" #include "smalloc.h" #include "vec.h" #include "copyrite.h" #include "statutil.h" #include "tpxio.h" what are they? and, where are they? thank you Lin /* * $Id: template.c,v 1.4 2001/07/23 15:28:29 lindahl Exp $ * *

[gmx-users] g_energy=> Different Average values from the screen than calculation of .xvg?

Hi After the command, g_energy -f abc.edr -o abc.xvg the average values is printed out on the screen. EnergyAverage RMSDFluct. Drift Tot-Drift Potential -267323 375.096 374.647 -0.12711 -63.5543 Kinetic En. 51901.5 259.034

[gmx-users] Different force field: Gromacs vs Autodock

Hi I use Gromacs (ffG45a3) to run MD in the protein vs ligand system. Then, I use Autodock to calculate the protein-ligand binding energy. As I know the force fields are different between ffG45a3 and Autodock. The two different force fields explain the same system. How can I explain this? Than

[gmx-users] Protein Activity

Hi How can I analyze / describe Protein Activity after MD simulation? Thank you Lin ___ 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

[gmx-users] Max notes = 256 ?

Hi But, I could not compile more than 256 notes when I run the Gromacs. Have anyone experienced compiling more than 1000 notes at one time? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

[gmx-users] Max nodes = 256 ?

Hi So, which version of Gromacs is more reliable for compiling 1000 nodes now? And, which version with higher computation load per node = computation efficiency? 4.0 4.0.2 4.0.3 4.0.4 Thank you Lin Chih-Ying Lin wrote: > > > > Hi > > But, I could not compile more than 256 no

[gmx-users] DSSP => MainChain+H group ?

d such don't matter for DSSP. Use the MainChain+H group for analysis." Why? What is the difference? Thank you Lin Chih-Ying Lin wrote: > HI > > 1. > type => > do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc > secondary-structure.xvg > >

[gmx-users] Protein Domain Motion

Hi Is it possible to simulate the Protein Domain Motion by MD ? Thank you Lin ___ 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 posti

[gmx-users] Protein Domain Motion

Hi I just check on line that the time scale for the Protein Domain Motion is micro-seconds. So, is it possible to simulate the Protein Domain Motion by MD? Thank you Lin Chih-Ying Lin wrote: > > > Hi > Is it possible to simulate the Protein Domain Motion by MD ? > Yes,

[gmx-users] How to start the Normal Modes Analysis?

Hi I read the Manual and still have no idea about the Normal Modes Analysis. How to start it? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

[gmx-users] Invalid command line argument: -np

Hi I typed the command => grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD5500.gro -p 6LYZ.top -o 6LYZ-MD6000.tpr It showed => Invalid command line argument: -np The above command works with 3.3.3 version but does not work with 4.0.5 version. I was checking grompp_mpi -h and cannot know the proper

[gmx-users] Invalid command line argument: -np

Hi Since the -np flag is no longer necessary with grompp for the version 4.0, how to tell Gromacs the number of the nodes being compiled together ? Thank you Lin Chih-Ying Lin wrote: > > > Hi > I typed the command => > > grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD55

[gmx-users] Invalid command line argument: -np

Hi The Gromacs version 4.0, there is no need of the flag -np for grompp So, Are the two following commands correct? grompp_mpi -v -f md.mdp -c 6LYZ-MD5000.gro -p 6LYZ.top -o 6LYZ-MD5500.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD5500 Thank you Lin Chih-Ying Lin wrote: > Hi > Since t

[gmx-users] use particle decomposition: mdrun -pd

Hi After the two commands, grompp_mpi -v -f minim.mdp -c 6LYZ.gro -p 6LYZ.top -o 6LYZ-EM-vacuum.tpr mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-vacuum Fatal error: pbc type no is not supported with domain decomposition, use particle decomposition: mdrun -pd What does it mean? Thank you Lin

[gmx-users] pbc = xyz with mdrun -pd ?

Hi I am setting pbc = xyz ; and type the commands grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated => the simulation failed and .out file suggested me to use the flag -pd. grompp_mpi -v -f minim.mdp -c 6LYZ-

[gmx-users] pbc = xyz with mdrun -pd ?

Hi I am setting pbc = xyz ; and type the commands grompp_mpi -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o 6LYZ-EM-solvated mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated => the simulation failed and .out file suggested me to use the flag -pd. grompp_mpi -v -f minim.mdp -c 6LYZ-

[gmx-users] A charge group moved too far between two domain decomposition steps

Hi In the system, one lysozyme + TIP3P water. After the two commands, grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-PR pr.mdp, minim.mdp and the error information is as follows. nsteps = 5000 ; Maximum number

[gmx-users] A charge group moved too far between two

out which steps I was doing wrong. Any ideas about this? Thank you Lin Chih-Ying Lin wrote: > > Hi > In the system, one lysozyme + TIP3P water. > > After the two commands, > grompp_mpi -v -f pr.mdp -c 6LYZ-EM-solvated.gro -p 6LYZ.top -o 6LYZ-PR.tpr > mpiexec -np 16

[gmx-users] A charge group moved too far between two domain decompostion steps

Hi A charge group moved too far between two domain decompostion steps What does this sentence mean? What is the domain decompostion step? How to make change about the domain decompostion steps? Thank you Lin ___ gmx-users mailing listgmx-users

[gmx-users] Gaussian network model (GNM) ?

Hi Is Normal mode analysis from Gaussian network model (GNM) ? Thank you Lin ___ 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 postin

[gmx-users] Can 3.3.3 and 4.0.5 version exist at the same time?

Hi The 3.3.3 and 4.0.5 version were installed under => * source /usr/gromacs/4.0.5/setup.sh source /usr/gromacs/3.3.3/setup.sh* *The 4.0.5 version is currently the default one.* I want to compare the computation results from 4.0.5 version and 3.3.3 version. So, I write the *source /usr/gromacs/3

[gmx-users] Bad water sampling ? => A charge group moved too far between two domain decomposition steps ???

Hi The system is "one lysozyme + water " running on 16 nodes. After => Energy minimization of the solvated systemRelaxation of solvent and hydrogen atom positions: Position restrained MDThen, the error was shown. --- Program mdrun_mpi, VERSION 4

[gmx-users] Minimisation - particle decomposition

Hi No matter pbc = no or pbc = xyz Energy Minimisation is required with particle decomposition. That is, mdrun -pd is required. Why? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

[gmx-users] The same lysozyme.pdb file under 3.3.3 and 4.0.5 version

Hi I was testing the same lysozyme.pdb file under 3.3.3 and 4.0.5 version under 16 nodes. Simply, lysozyme.pdb + water. There is no problems (errors) with 3.3.3 version. However, with 4.0.5 version, the same lysozyme pdb file with the same simulation condition. except mdrun -pd with minimisation

[gmx-users] template.c

Hi : I have difficulties to understand the following three files, which are in Gromacs Package. 1. template.c 2. README 3. Makefile.x86_64-unknown-linux-gnu Please tell me if I have to do part 3 to compile template.c. Thank you Lin = [ TEMPLATE.C ] ==

[gmx-users] template.c => put the GROMACS headers in the same file ?

Hi Following are 1. template.c 2. README 3. Makefile.x86_64-unknown-linux-gnu In the template.c => it includes several GROMACS headers. #include "statutil.h" #include "typedefs.h" #include "smalloc.h" #include "vec.h" #include "copyrite.h" #include "statutil.h" #include "tpxio.h" If I put t

[gmx-users] template.c

d => ./template < template.in Am I right? Thank you Lin Chih-Ying Lin wrote: > Hi > Following are > 1. template.c > 2. README > 3. Makefile.x86_64-unknown-linux-gnu > > > In the template.c => it includes several GROMACS headers. > #include "statutil.h&qu

[gmx-users] Can Gromacs produce the data from NMR?

HI Can Gromacs produce the data from NMR? Thank you Lin ___ 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

[gmx-users] g_msd ?

Hi # g_msd_mpi is part of G R O M A C S: # # Giant Rising Ordinary Mutants for A Clerical Setup # @title "Diffusion Coefficients / Molecule" @xaxis label "Molecule" @yaxis label "D" @TYPE xy 00.907803 1 3.5355 2 4.34231 3 3.83589

[gmx-users] trjconv => not get the enough data ?

Hi in my .mdp file, i set up the total 4000 times saving the coordinates of each atom. then, I use the command trjconv -f xx.gro -s xx.tpr -o xx-traj.gro then, i checked the xx-traj.gro file and found there were less than 4000 times of recording coordinates for each atom. say 3600 times of

[gmx-users] g_dipole ? => dipole moment ?

Hi I issue the g_dipole command on Gromacs => And, the following information is shown. There are 10 molecules in the selection, Does the Average =32.1611 refer to the average for a single over the simulation time? Or, the Average = 32.1611 summing for all the 10 molecules over the simulation time?

[gmx-users] g_dipole ? => dipole moment ?

oment around 32 is acceptable? Thank you Lin On 2010-10-16 21.36, Chih-Ying Lin wrote: > > Hi > I issue the g_dipole command on Gromacs => And, the following > information is shown. > There are 10 molecules in the selection, > Does the Average =32.1611 refer to the ave

[gmx-users] g_dipole ? => dipole moment ?

s center of atom from the mass center of the molecule? 4. What does the large charge separation mean? Do you mean the charged molecule? Or, Do you mean the molecule with a long carbon chain? Thank you Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: > HI > I confined one molecule in the c

[gmx-users] g_dipole ? => Calculate bond dipole moment for a molecule of multiple atoms by hand?

ou Lin On 2010-10-18 03.30, Chih-Ying Lin wrote: > HI > I confined one molecule in the center of box and issue the g_dipole command. > The average dipole moment is still around 32. > It is the molecule with 33 atoms / united atoms of most carbon groups, > isn't the dipole

[gmx-users] g_dipole ? => ionic bond => how to determine the direction of ionic bond dipole moment ?

calculator in about 10min. Do not worry about the reference point as long as your system is neutral, just set it to (0,0,0). Otherwise, take any kind of first year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: > > > Hi > Acco

[gmx-users] g_dipole ? => what is the bond length of the ionic bond in the dipole moment calculation?

st year physics book it will contain very similar information. On 10/19/2010 05:39 AM, Chih-Ying Lin wrote: > > > Hi > According to the following website, > > http://en.wikipedia.org/wiki/Bond_dipole_moment > > > \mu = \delta \, d. > The bond dipole is modeled as

[gmx-users] g_dipole ? => salt molecule in water => what is the the displacement vector pointing from the negative charge to the positive charge?

to one counter ion and the rest of the molecule in water? http://en.wikipedia.org/wiki/Bond_dipole_moment http://en.wikipedia.org/wiki/Electric_dipole_moment Thank you Lin On 2010-10-20 06.06, Chih-Ying Lin wrote: > > > > > Hi > molecule dipole is 48.0 sum of q_i x_i &

[gmx-users] g_dipole ? => salt molecule in water => should I include counter ions in my calculation?

HI 48.0 sum of q_i x_i x_i is the atomic position. For the salt molecule in water, should I include counter ions in my calculation ? Or, only the rest of the salt molecule except the counter ions? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here "A" are a string of atoms, most of them are carbons. For the cis-structur

[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

I wouldn't include the bromide if I were you, as it just adds noise, because it can move around freely. You seem to be interested in the change in dipole moment in the cation only, anyway. Cheers, Tsjerk On Oct 21, 2010 7:02 AM, "Chih-Ying Lin" wrote: HI dipole moment = 48.0 sum of

[gmx-users] g_dipole ? => dipole moment => trans-structure is more hydrophobic than the cis-structure ?

Hi In one paper, the salt-molecule has two structures, trans and cis. The sentence in the paper is that trans-structure is more hydrophobic than the cis-structure without providing the value of the dipole moment. I wonder know if the value of dipole moment is the main indicator to decide if tran

[gmx-users] g_dipole ? =>salt-molecule => the relative position of counter ions to the rest of salt-molecule matters ???

HI As Timo M.D. Graen described "As long as the system is neutral, the reference point will not affect the calculation result of the dipole moment for the system." On the other hand, I also play around the small salt-molecule as Timo M.D. Graen suggested. "take two ions for a start, Na+ and Cl-,

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