[gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)

.itp. How to do "Proper parameterization" with a more understandable method? If the solution is very dilute, Br - ions will have very limited power affecting the whole system, I suppose. Are there any alternative ways to solve the problem ? Thank you Lin Chih-Ying Lin

[gmx-users] Water model => amber port to gromacs

Hi Water model => amber port to gromacs The two steps are shown on the archive. 1. #include ffamber_tip*pin the .top file 2. include an #ifdef_FF_AMBER statement in tip*p.itp Should I also #include ffamber99.tip in the .top file? Thank you Lin __

[gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)

3.76560e-01 Does it make sense? Thank you Lin Chih-Ying Lin wrote: > Hi > In the ions.itp, there is no BR- ion defined (FF_Gromos 96). > > But, it was defined in FF_OPLS. > > How did people solve the problem? > Could I simply use all of BR-atom (assign it a

[gmx-users] Water model => amber port to gromacs

ove links. 1. #include ffamber_tip*pin the .top file 2. include an #ifdef_FF_AMBER statement in tip*p.itp Should I also #include ffamber99.itp in the .top file? Thank you Lin Chih-Ying Lin wrote: > Hi > Water model => amber port to gromacs > > The two steps are shown o

[gmx-users] Water model => amber port to gromacs ? => OR Only SPC ?

Hi Can the TIP3P water model used under gromos 96 force field? Although the Amber_TIP3P.top can port to gromacs, it based on the amber99 force field. I read about the imcompatibility of any two force field parameters from different sources, such as amber99 and gromos96. Is Gromacs only limited t

[gmx-users] Water model => amber port to gromacs ? => OR

HI The thing is the definition of atom type, OW and H in gromos 96 are different from tip3p.itp, OWT3, HW. same thing as other tip*p.itp. How to fix this? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/

[gmx-users] genbox -ci solute.gro -nmol N

Hi Originally, in the topol.top file => [molecule] solute 1 After the command: genbox -cp one_solute.gro -cs spc216.gro -ci one_solute.gro -nmol N -p topol.top in the topol.top file => [molecule] solute 1 solvent 5000 I think the flag "-p topol.top" in the genbox command did not do it corr

[gmx-users] Concentration

Hi How to make a solution with specific concentration ? Command 1 => editconf -d 0.75 -bt cubic 0.75=Distance between the solute and the box cubic = the type of the simulation box Command 2 => genbox -cp solute.gro -cs spc.gro -box Y Y Y Y = the box vector in nm If I use cubic in my system, i

[gmx-users] the solute out of water box

Hi What does it mean "the solute running out of water box" ? Did it mean that my simulation fail? How to fix this problem? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] editconf -density 1000

Hi The flag of editconf -density has the default value 1000 editconf -densityreal1000Density (g/l) of the output box achieved by scaling But, my system is running on D2O not H2O Earlier I did not notice this flag and simply use the command editconf to create a box. So, will my sim

[gmx-users] How to center one - solute in the water box?

Hi the command editconf -center 0, 0 , 0 This command will make the water system center (0,0,0). How to put one-solute in the center of the water box? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/l

[gmx-users] How to calculate the thermodynamic properties of the solution?

HI How to calculate the thermodynamic properties of the solution? The thermodynamic properties of the solution, for example, entropy, delta S enthalpy, delta H Gibbs free energy, delta G free energy, delta nu How to extract the thermodynamic properties from the MD simulated system? Thank you Lin

[gmx-users] Light-controlled MD

HI Some surfactants can be light-controlled. Could anyone directed me how to simulate the light-controlled surfactants system with MD? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] How to determine if it is the pi-pi stacking interaction?

Hi How to determine if it is the pi-pi stacking interaction? My system are surfactants mixing with water. The surfactants carries phenyl-groups. Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] After MD simulation => put the sample under Scattering

Hi Has someone experineced put "the MD-simulated sample" under "a modeled -scattering equipment" ? Or, how to "model a scattering equipment" ? then, how to put the sample under the modeled scattering equipment? Or, how to get the scattering data from the MD-simulated system? Thank you Lin

[gmx-users] After MD simulation => put the sample under

SANS? Thank you Lin Chih-Ying Lin wrote: > Hi > Has someone experineced put "the MD-simulated sample" under "a modeled > -scattering equipment" ? > > > Or, how to "model a scattering equipment" ? > then, how to put the sample under the mod

[gmx-users] Simulation Techniques

Hi There are lots of simulation techniques, which are much beyond what I have learned from the Gromacs manual and Gromacs Tutorials. Those are Monte Carlo, kinetic dynamics, QM/MM, scattering, sampling, photo-controlled.. I read some books and some papers. but in fact I could not figure

[gmx-users] MD vs Scattering

Hi Can we simulate "samlple putting on the equipment using GROMACS-MD package"? 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/searc

[gmx-users] MD vs Scattering

Hi Can running MD to reproduce the data from scattering? If so, How? 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 p

[gmx-users] How to show the created box?

HI after creating the box, and write it into .gro file. when i try the .gro file with VMD, but the box is not shown. how can i show the created box with VMD? thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mai

[gmx-users] NVT or NPT ?

HI I read some papers and it seems that more simulation system is under NPT. What is the benefit for running MD under NPT? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] where is the position of the partial charges?

Hi where is the position of the partial charges? Is it in the center of the atom? As one user of Gromacs, I can assign or write the partial chage for each atom in the .top file. How about changing the position of the partial charge? Thanks Lin ___ gm

[gmx-users] How can I record only molecule trajectory ?

Hi The command mdrun -o traj.trr -x traj.xtc and then, the two files, traj.trr or traj.xtc will record the trajectory of all the molecules of the simulated system. How can I record only molecule trajectory with some command? Thank you Lin ___ gm

[gmx-users] PDB structure quality

HI The program WHATIF can perform a proper validation of the structure. But, it is not free software. Can anyone tell me how to test the protein structure manually or by Gromacs? What is the criteria to determine the quality of the structure? Thank you Lin ___

[gmx-users] Remove the water from the crystal structure of Protein in PDB file

Hi The protein is in the crystal structure. So, the PDB file includes some water molecules. Could I just remove those water molecules?? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-user

[gmx-users] The free energy calculation in Manual Chapter 4

Hi I read the free energy calculation in Manual Chapter 4. What condition could I use this free energy calculation of the Gromacs MD package? >From tutorial, the solvation free energy can be calculated by Gromacs. how about the free energy of the micelle forming system? Can i apply the free energ

[gmx-users] Force field parameters in water or in vacuum?

Hi For one molecule, will Gromacs give the same set of force field parameters to this molecule no matter this molecule is put in water or in vacuum? The bond length, the bond angle, and the dihedral angles of the same molecule will be different in water and in vacuum. So, will the force field param

[gmx-users] Simulate the organic molecule => input / output error

Hi Does the Gromacs only recognize the residues in the pdb file? If they are not the standard amino acids in the library, Gromacs can't read, right??? Or, how does the Gromacs simulate the organic molecule? The command pdb2gmx could not produce the top and the gro file. Instead, it shows that "

[gmx-users] Re: Force field parameters in water or in vacuum?

emkul" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Force field parameters in water or in vacuum? To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Quoting Chih-Ying Lin <[EMAIL PROTECTED]>: > Hi > For one mo

[gmx-users] How to calculate dihedral angle ??

HI g_chi is designed to help user to calculate the dihedral angles. I have an organic compound and as the manual describes that .gro , .trr and ssdump.dat are the required input files to compute and collect the dihedral angles with time. For my case, .gro and .trr files are ready. How to prepar

[gmx-users] Re: How to calculate dihedral angle ??

in; charset=ISO-8859-1; format=flowed Chih-Ying Lin wrote: > > HI > g_chi is designed to help user to calculate the dihedral angles. > > I have an organic compound and as the manual describes that .gro , > .trr and ssdump.dat are the required input files to compute and > collect

[gmx-users] Have read the manual => How to calculate dihedral angle??????

HI I have read the manual but the thing is that I could not get the answers from the manuals. So, I repeatly ask the same questions and if anyone could give me the exact answers. Thanks a lot. Lin I use mk_angndx to produce angle.ndx then, enter g_angle -od angdist.xvg -ov anga

[gmx-users] The dihedral angles from 192 elements ??

Hi Four atoms form a set of diheral angles. When I do g_angle for the dihedral angle calculation, it shows Group 0 (Phi=180.0_2_70) has 4 elements Group 1 (Phi=180.0_2_6) has16 elements Group 2 (Phi=180.0_2_40) has 192 elements Select a group: If I select Group 2, there is

[gmx-users] Dynamics : ONE dihedral angle time resolution

Hi I want to get the dynamics of ONE dihedral angle time resolution. g_angle computes the angle distribution for a number of angles or dihedrals. With option -ov I can plot the average angle of a group of angles as a function of time. I don't want the average angle of a group of dihedral angle as

[gmx-users] the .mdp format

Hi I did not fully understand about this command. Could anyone explain this more? Thanks a lot include: directories to include in your topology. Format: -I/home/john/my_lib -I../more_lib Lin ___ gmx-users mailing listgmx-users@gromacs.org http://ww

[gmx-users] .mdp format

Hi if I am in my working directory, and give the command in my .mdp file include =-I/my_working_directory I will get the following error Program grompp, VERSION 3.3.3 Source code file: grompp.c, line: 469 Fatal error: number of coordinates in coordinate file (xxx.gro, 24)

[gmx-users] Re: .mdp format

TED]> wrote: > > > Chih-Ying Lin wrote: > > > Hi > > if I am in my working directory, > > and give the command in my .mdp file > > > > include =-I/my_working_directory > > > > > > I will get the following error > >

[gmx-users] Force Field: A new chemical compound

Hi Honestly, I don't know how to do the quantum chemistry calculation. I have the one azobenzene derivative force field parameters(from QM/MM paper) in hand. This azobenzene derivative is quite similar with the azotab compound, which I need. For the rest parts of the azotab compound I try to used

[gmx-users] mdrun -nice integer

Hi for the mdrun command, what does "-nice integer" mean? I have read the manual, but still have no idea for this. Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive

[gmx-users] box size

Hi 1. in the last row of .gro file, the three number represent the length of the box on X, Y , and Z directions in nanometer. Right?? 2. for the editconf command, editconf -d Distance_between_the_solute_and_the_box bt cubic Right?? what are the differences between the three number in th

[gmx-users] simulate Gas Phase system

Hi to simulate the gas phase system, before running MD on the gas phase system I have to use the "editconf" command. But, I DO NOT use "genbox" command. Right?? thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mail

[gmx-users] .mdp format

Hi An example of the .mdp file format is as follows. tau_t= 0.1 0.1 ref_t= 300 300 why are the tau_t and ref_t owning two values separately? thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http:/

[gmx-users] Wilson angle

Hi I want to calculate the wilson angle. but, I am not sure if the wilson angle is the same as the improper dihedral angle. Could anyone tell me this? then , to calculate the wilson angle, use the command, like: g_angle -type improper Thanks Lin ___ g

[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling

Hi My system has been dealt with minimisation and the system was kept constant at 0 K. Then, I want to increate the temperature to 300 K using the Berendsen thermostat. Should I increase the temperature of the system step by step... ? increase temp from 0 K to 50 K 5

[gmx-users] what is cgnr ?

Hi In the .top file, [atoms] section, cgnr is given. Could any one explain more about the cgnr? Manual does not say it more. Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please se

[gmx-users] The WARNING

HI WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Is this warning serious? Could any one tell me how to fix the warning? I see nothing wrong with my .top and my .gro file. Thank you Lin

[gmx-users] pdb file ???

Hi It is the water-molecule system. For a molecule, like R-N(CH3)3-Br, I could make a pdb file either include Br ion or exclude Br ion. If I exclude Br ion, I have to make Br ion as the counter ion for my system. If I include Br ion, I do NOT have to make Br ion as the counter ion since it will

[gmx-users] cgnr

Hi As Justin described, cgnr = charge group number could anyone explain more about this ? and, how to determin cgnr? Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] Salt molecule - ion bond

Hi The salt R-N(CH3)3-Br. Could anyone tell me how to assign the force field parameter for the salt molecule ; especially for the ion bond/ ion angle/ Does there exist "dihedral angle " between the ion Br and R ? And, any differences for assigning the Van-der waal and LJ parameters between salt a

[gmx-users] The WARNING

Hi As you described... This is not a grompp warning, but a warning from one of the analysis tools. grompp will never take masses 'out of the blue', but will always use the force field description (atom type definitions) or the mass specified in the .top/.itp file. It will bail out if no mass is

[gmx-users] g_sgangle

Hi In manual, it says. -oa: Angle between the two groups specified in the index file. If a group contains three atoms the normal to the plane defined by those three atoms will be used. If a group contains two atoms, the vector defined by those two atoms will be used. one group contains 3 at

[gmx-users] g_angle , g_bond distribution

Hi I used g_angle , g_bond to obtain the angle and bond distribution. But, I don't know if the distribution has been normailzed or not. how is the distribution from? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.or

[gmx-users] g_energy

Hi I use g_energy to calculate the total energy for the system. what is the unit for the total energy? and, how could I convert it to kJ/mole ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] #include "ffG45a3.itp"

HI 1. when i make a .top file myself, i wrote the command #include "ffG45a3.itp". with this command, does it mean that Gromacs will assign the force field parameters automatically for those I do NOT write into the .top file ? 2. the complete data for ffG45a3 are as follows If I simply write "#inc

Re: [gmx-users] #include "ffG45a3.itp"

Or, I have to include all of them in my .top file. ffG45a3.itp ffG45a3.ddb ffG45a3.hdb ffG45a3.rtp ffG45a3bon.itp ffG45a3nb.itp ffG45a3-c.tdb ffG45a3-n.tdb ffG45a3.atp Chih-Ying Lin wrote: > HI > 1. when i make a .top file myself, i wrote the command #include "ffG45a3.itp&q

[gmx-users] The molecular structure

Hi the molecular structure : bond length, bond angle, dihedral angle the bond length, bond angle are easily determined.. but the dihedral angle are hard to control... with one set of the force field parameter, I could not get the exact structure of the molecule (not all of the dihedral ang

[gmx-users] CPMD- QM MM simulation

Hi I read some papers, which the authors use CPMD - QM MM simulation to reparametrize the force field parameters. But, they did not say the details. Could anyone explain this more here? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] D2O

Hi Does Gromacs support D2O simulation? Is it any difference between the D2O and H2O except the molecular weight? and, how about the force field parameters? are the two systems just the same? Thank you Lin ___ gmx-users mailing listgmx-users@groma

[gmx-users] D2O

Hi I would like to simulate the solutes are embeded in D2O solution. Could someone explain the difference of simulating D2O solution and H2O solution? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/list

[gmx-users] the FF parameter sets

Hi I am looking into the FF parameter sets from the FF.itp. for example #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 I could not understand the last line. Please tell me what it means. Thank you Lin ___ gmx-users mail

[gmx-users] the FF parameter sets

Hi I think that I did not described my question clearly. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 three atoms A, B, C form an angle. A-B-C what does this line mean? H - N - CH3. H, HC-6-ring, H-NT-CHn 90 does it mean ? =>H - N - CH3 H - N - H, H - N

[gmx-users] the FF parameter sets

Hi I have to ask the same question again. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring, H-NT-CHn 90 I confuse with the comma "," and " - " does it mean ? =>H - N - CH3 ( the angle between H - N - CH3, right?) H - N - H, H - N - (HC-6-ring) H - N - CHn 90 (HC-6-r

[gmx-users] the FF parameter sets

Hi I read your comment. "This is a comment line to the previous one. The angle is between the three atoms mentioned. it is an index in another array in the gROMOS96 files (not part of gromacs) ." But, I did not understand.. #define ga_24 120 505 ; H - N - CH3. H, HC-6-ring

[gmx-users] g_sas => micelle ?

HI how to calculate SASA of micelle using g_sas? i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the atom numbers of micelle. if micelle is not compact enough but there are no water molecules inside the micelle, will g_sas calculate the vacancy part inside the micelle? Or,

[gmx-users] g_sas => protein and ligand aggregate interface area ?

HI As David said, => How to compute protein-protein interface area? "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" I want to calculate protein and ligand aggregate (small micelle of ligand) interface area. Is it the same step as calcu

[gmx-users] g_sas -pbc ???

Hi g_sas By default, periodic boundary conditions are taken into account. How does g_sas deal with periodic boundary conditions effects? ? ? Take trjconv an example, I have tried trjconv -pbc ( nojump , whole, atom... ) or, trjconv -center . I could not get what i wanted. Thank you Lin -- gmx

[gmx-users] trjconv => -[no]vel => print out the velocity ?

Hi Trjconv => with option "- [no] vel " what does the bracket "no" mean ? with the following command, trjconv -f MD.trr -s MD.tpr -vel -o MD-test.gro the velocity is not print out on MD-test.gro. How to print out both the velocity and trajectory at the same time from .trr file? THank y

[gmx-users] g_gyrate -p => Calculate the radii of gyration about the principal axes

Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got => 0.922754 1.22249 1.25603 but in some paper, the authors got => 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the

[gmx-users] g_gyrate -p => the radii of gyration about the principal axes ?

Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got => 0.922754 1.22249 1.25603 but in some paper, the authors got => 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the

[gmx-users] g_gyrate -p => the radii of gyration about the principal axes ?

tein molecule is a standard process ? => I mean the principal axes of the protein molecule is fixed, right ? => I mean the math of the principal axes of the protein molecule is defined all over the world , right ? Thank you Lin On 2010-08-14 23.49, Chih-Ying Lin wrote: >

[gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

Hi Execute g_sas to get protein interface >From David => "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" WHy not HALF of (A+B-AB) ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

Hi The partial charges of the trans and cis azobenzene are given as point charges lied on each atom center in my MD simulation. It is supposed that the real molecule of trans-azobenzene has a lower dipole moment than the cis one. So, the real molecule of trans-azobenzene is supposed to be more hy

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

HI The charges of azobenzene from the authors, who made the QM/MM simulations and fit some experimental data about the azobenzene. Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: > > Hi > The partial charges of the trans and cis azobenzene are given as point > charges

[gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

Hi Execute g_sas to get protein interface >From David => "If you have protein A and B in complex you do three g_sas: AB AB A A B B the interface is now A + B - AB" WHy not HALF of (A+B-AB) ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/li

[gmx-users] dipole moment of molecule of trans and cis azobenzene ?

HI >From David => dipole moment = mu = sum_i q r. is that sum of partial charges * r ? what is the " r " ? Thank you Lin On 2010-08-26 18.59, Chih-Ying Lin wrote: > > Hi > The partial charges of the trans and cis azobenzene are given as point > charges lied

[gmx-users] g_sas => calculate the SASA for each residues ?

Hi How can I calculate the SASA for each residue ? >From Manual => "The program will ask for a group for the surface calculation and a group for the output." When I issue the command => g_sas -f abc.gro -s abc.tpr -n Residue1.ndx -o SASA.xvg => Gromacs will pick Residue1.ndx as both a grou

[gmx-users] Force Field => Residues PHE, TRP, TYR, HIS ?

HI Residues PHE, TRP, TYR, and HIS are carrying "Rings", or say pi bonds. How does the Gromacs deal with polarity for all this four residues? Is a single charge assigned for each atom on the center of atoms of the four residues ? Is pi bond given for the four residues in the force field? Tha

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