[gmx-users] tfe.gro

Hi, Does anyone have the tfe.gro for solvent box? I have the tfe.itp file in /usr/share/gromacs/top/ directory. [ atoms ] 1 C 1 TFE C 1 0.74 2 F 1 TFE F 1-0.25 3 F 1 TFE F

Re: [gmx-users] changing the velocity in trajectory file

On Nov 29, 2010, at 8:52 PM, sreelakshmi ramesh wrote: > Lutz ya you are true but as you said how can i change the velocity for a > config every move as in TPS?since i have not done tps i have no idea abt this. You can't, neither for TPS nor for FFS. I don't think Gromacs provides this function

Re: [gmx-users] changing the velocity in trajectory file

Lutz ya you are true but as you said how can i change the velocity for a config every move as in TPS?since i have not done tps i have no idea abt this. sree On Tue, Nov 30, 2010 at 9:15 AM, Lutz Maibaum wrote: > On Nov 29, 2010, at 5:58 PM, sreelakshmi ramesh wrote: > > Basically i have been

Re: [gmx-users] changing the velocity in trajectory file

On Nov 29, 2010, at 5:58 PM, sreelakshmi ramesh wrote: > Basically i have been using a sampling method called FFS to calculate the > rate constant for folding of a protein .The umbrella sampling done on the > system shows there is high barrier between the reac an prod states The phase > spece r

Re: [gmx-users] changing the velocity in trajectory file

chris.ne...@utoronto.ca wrote: Sorry sree, it still sounds like you want grompp with gen_vel=yes , as others have suggested. You're going to need to explain it better if you want to get more help. If you are saying that you need to *slightly* randomize the velocities but not change them as

Re: [gmx-users] What does "Conserved-En." stands for

Thanks a lot, Michael. -- Jim On Mon, Nov 29, 2010 at 1:02 PM, Michael Shirts wrote: > For integration schemes like Nose-Hoover that are not NVE but have > some other quantity that is conserved, then "Conserved-En. provides > the value of this conserved quantity. > > > Michael Shirts

[gmx-users] changing the velocity in trajectory file

Sorry sree, it still sounds like you want grompp with gen_vel=yes , as others have suggested. You're going to need to explain it better if you want to get more help. If you are saying that you need to *slightly* randomize the velocities but not change them as much as by total reassignment,

Re: [gmx-users] changing the velocity in trajectory file

so everytime when the same trajectory file is read is it possible to randomize the velocity by a small amount so that i may end up with different trajectory? sree. On Tue, Nov 30, 2010 at 7:28 AM, sreelakshmi ramesh < sree.laks...@research.iiit.ac.in> wrote: > Basically i have been using a sampl

Re: [gmx-users] changing the velocity in trajectory file

Basically i have been using a sampling method called FFS to calculate the rate constant for folding of a protein .The umbrella sampling done on the system shows there is high barrier between the reac an prod states The phase spece regions in ffs method are divided in to many non -intersecting int

Re: ?????? [gmx-users] How to save the coordinates of all atoms in the 2D-ar rays using xdrfile?

On 30/11/2010 11:10 AM, wrote: Dear Mark, Thank you for your reply. It seems reasonable to deal with a frame at one time. But in my code, the coordinates in two different frames are frequently required to compare to each other. Other part of this code is like g_msd which calculate

回复： [gmx-users] How to save the coordinates of all atoms in the 2D-arrays using xdrfile?

Dear Mark, Thank you for your reply. It seems reasonable to deal with a frame at one time. But in my code, the coordinates in two different frames are frequently required to compare to each other. Other part of this code is like g_msd which calculates the mean-squared displacements for the at

Re: [gmx-users] perl script for g_hbond

Hi. Did you inspect the contents of hbmap.xpm? There's a header followed by matrix data. You can think of the matrix as ones and zeroes, represented by the characters 'o' (= one) and ' ' (space = zero). As such, the rows of the matrix are vecors containg ones and zeroes. Two such vectors can

Re: [gmx-users] Attractive and repulsive components of Pot energy

On 30/11/2010 4:20 AM, Sai Pooja wrote: Hi, Is there a way to extract the attractive and repulsive parts of the LJ interactions in a simulation? No. They're added immediately they've been calculated in the non-bonded kernels. Your only sensible recourse is to hack the .top to have suitable

Re: [gmx-users] changing the velocity in trajectory file

On 30/11/2010 2:16 AM, sreelakshmi ramesh wrote: so can anybody tell me how to hack the trr file so that i can change the velocity parameter in it You've expressed no reason to need to do that rather than generate independent random sets of velocities. If you're going to ignore the advice you

Re: [gmx-users] charge group radii

On 30/11/2010 2:25 AM, Gavin Melaugh wrote: Cheers Mark for the reply I was more concerned about the Van der Waals interactions. If the distance between the centre of geometry of two charge groups is larger than rlist then these interactions are not included. I was therefore concerned if I had a

Re: [gmx-users] changing the velocity in trajectory file

On Mon, Nov 29, 2010 at 16:16, sreelakshmi ramesh wrote: > so can anybody tell me how to hack the trr file so that i can change the > velocity parameter in it You can use the xdrfile library to read in a certain frame of the trr file, change the velocity in the array that you get, then use the xd

Re: [gmx-users] C6 attractive term off OPLSAA

Okay I am going to give it a try. I just wanted to make sure I was calculating C6 and C12 correctly as well using sigma and epsilon according to rule 3 C12 = Sigma^(6)*C6 C6 = 4*sigma^(6)*epsilon Thanks Quoting "Justin A. Lemkul" : nishap.pa...@utoronto.ca wrote: Hello, I have a co

Re: [gmx-users] C6 attractive term off OPLSAA

nishap.pa...@utoronto.ca wrote: Hello, I have a concern regarding C6 attractive term in LJ potential. I am using OPLS-AA force field, and I wish to turn off attractive term C6 by setting the parameters to zero. One of the suggestion was to add a [nonbond_params] in my ffoplsaanb.itp file

[gmx-users] C6 attractive term off OPLSAA

Hello, I have a concern regarding C6 attractive term in LJ potential. I am using OPLS-AA force field, and I wish to turn off attractive term C6 by setting the parameters to zero. One of the suggestion was to add a [nonbond_params] in my ffoplsaanb.itp file and set the C6 to zero betwee

Re: [gmx-users] What does "Conserved-En." stands for

For integration schemes like Nose-Hoover that are not NVE but have some other quantity that is conserved, then "Conserved-En. provides the value of this conserved quantity. Michael Shirts Assistant Professor Department of Chemical Engineering University of Virginia michael.shi...@virg

[gmx-users] g_rama problem about dihedrals

Hello, I have an old trajectory simulated using the Charmm force field and I would like to get the Phi/Psi dihedral combinations as a function of time, using g_raman. I am using a single pdb to start with. I created a topology for this pdb using: pdb2gmx -f protein.pdb -o protein_gmx.pdb -p top

[gmx-users] What does "Conserved-En." stands for

Dear all: When using g_energy to analyze the energies of the MD system, an entry termed "Conserved-En." is provided. What does this term stands for? The simulation is in NVT ensemble. Thanks, RQ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-use

[gmx-users] Attractive and repulsive components of Pot energy

Hi, Is there a way to extract the attractive and repulsive parts of the LJ interactions in a simulation? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

Re: [gmx-users] perl script for g_hbond

Dear Justin, Thank you very much. best, Olga 2010/11/29 Justin A. Lemkul > > > Olga Ivchenko wrote: > >> Hi Leila, >> >> I am also have a task to calculate H-bonds frequency through the over all >> trajectory in gromacs. Please can you send me Justin's script. If he does >> not mind. >> >> > I

Re: [gmx-users] charge group radii

Cheers Mark for the reply I was more concerned about the Van der Waals interactions. If the distance between the centre of geometry of two charge groups is larger than rlist then these interactions are not included. I was therefore concerned if I had a situation in which certain atoms of a charge

Re: [gmx-users] changing the velocity in trajectory file

so can anybody tell me how to hack the trr file so that i can change the velocity parameter in it On Mon, Nov 29, 2010 at 8:40 PM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> so if i use gen_vel = yes ad seed -1 i get diff traj.But what would happen >> if read the postion and ve

Re: [gmx-users] changing the velocity in trajectory file

sreelakshmi ramesh wrote: so if i use gen_vel = yes ad seed -1 i get diff traj.But what would happen if read the postion and velocity from traj file(input file) When you supply a .trr file in conjunction with "gen_vel = yes," the position is taken but the velocities are ignored. grompp te

Re: [gmx-users] changing the velocity in trajectory file

so if i use gen_vel = yes ad seed -1 i get diff traj.But what would happen if read the postion and velocity from traj file(input file) On Mon, Nov 29, 2010 at 8:08 PM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> i am reading the velocities from trajectory file.so i dont want the

Re: [gmx-users] perl script for g_hbond

Olga Ivchenko wrote: Hi Leila, I am also have a task to calculate H-bonds frequency through the over all trajectory in gromacs. Please can you send me Justin's script. If he does not mind. I have several analysis scripts available to the public on my website: http://www.bevanlab.biochem

Re: [gmx-users] perl script for g_hbond

Hi Leila, I am also have a task to calculate H-bonds frequency through the over all trajectory in gromacs. Please can you send me Justin's script. If he does not mind. Yours sincerely, Olga 2010/11/29 leila karami > Dear Mark and gromacs users > > thanks for your time and consideration. > > yo

Re: [gmx-users] pdb file problem

benrezkallah djamila wrote: Hello Everybody; I have a problem with The 2PU3 pdb entry (download from www.rcsb.org ) ; the download file gives for certain residues such as residu 25 : SER (and others in the pdb file), two different positions for the atoms of the residu.

Re: [gmx-users] changing the velocity in trajectory file

sreelakshmi ramesh wrote: i am reading the velocities from trajectory file.so i dont want the maxwellain distribution of veloc thats y i have set gen_vel=no. Generating velocities is the only way to get new ones to start independent trajectories. Otherwise, you'd have to somehow manually

[gmx-users] perl script for g_hbond

Dear Mark and gromacs users thanks for your time and consideration. you said by multiplying the existence functions for hbonds between protein and water and the hbonds between water and DNA, then using Justin's script, I can obtain percentage each water medited hydrogen bond during trajectory. an

Re: [gmx-users] changing the velocity in trajectory file

i am reading the velocities from trajectory file.so i dont want the maxwellain distribution of veloc thats y i have set gen_vel=no. sree On Mon, Nov 29, 2010 at 7:32 PM, Baofu Qiao wrote: > > Why don't use different random (gen_vel =yes; gen_seed =-1 in .mdp > file) seed to generate the veloc

[gmx-users] Re: error in grompp command

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private help service. I am CC'ing the list and would ask that all further discussion occur there. rasmiprava samal wrote: ERROR 1 [file topol.top, line 20758]: No default Ryckaert-Bell. types You have

Re: [gmx-users] changing the velocity in trajectory file

Why don't use different random (gen_vel =yes; gen_seed =-1 in .mdp file) seed to generate the velocity? On 11/29/2010 02:55 PM, sreelakshmi ramesh wrote: > Dear all, > could anybody help me out with the following issue. I have a > trajectory file.i have to used that file at a par

[gmx-users] changing the velocity in trajectory file

Dear all, could anybody help me out with the following issue. I have a trajectory file.i have to used that file at a particular frame as the input to continue the simulation and i need to use that file for 20 independent simulations.since the starting file for the 20 simulations are

Re: [gmx-users] charge group radii

On 26/11/2010 3:01 AM, Gavin Melaugh wrote: Hi all, I have recently been testing out the new version of Gromacs. To do so I have used files from previous simulations in Gromacs-4.0.7. When feeding the three files (mdp,gro, and top) into grompp, the following note is displayed: NOTE 3 [file pbc.

Re: [gmx-users] How to save the coordinates of all atoms in the 2D-arrays using xdrfile?

On 28/11/2010 12:12 AM, wrote: Dear gmxers, I am trying to perform an analysis on the trjectory file using xdrfile library. First of all, I want to save the coordinates of all atoms in three 2D-arrays, i.e. xx[step-1][natom-1], yy[step-1][natom-1], zz[step-1][natom-1]. How to do s

[gmx-users] Re: Re: Error while using forcefield GROMOS 43a1p (Justin A. Lemkul)

Dear Justin I got the solution. I forgot to add residue types in residuetypes.dat Anyway thanks for your kind reply with regards, Jignesh Patel On Mon, Nov 29, 2010 at 12:17 PM, Jignesh Patel wrote: > > Dear Justin, > > Thanks for your reply. > I have checked whole pdb file. Everything is f