[gmx-users] harmonic restraint

Dear all GROMACS users, I'm new in protein simulation. Does anybody let me know in what subroutine the harmonic restraint is implemented? If I would like to trace back to the subroutine from md.c, how can I do that? I really appreciate any comments on such a beginner's question. Best, Jae H. Pa

Re: [gmx-users] sampling conformation on the basis of RMSD value

Hi there, below you can find a "dirty" perl script that I used to extract structure from a trr by reading the cluster.log file from g_cluster Just remove in the cluster.log file all the lines until the (included): cl. | #st rmsd | middle rmsd | cluster members # paste from here --

Re: [gmx-users] simulation in vacuum

David is right! There are no FF that has been parametrized for vaccum simulations and the best you can do is using a classical FF and neutralize charges to avoid collapses ... be aware of what you do ... On Wed, 17 Sep 2008 19:13:33 +0200 David van der Spoel <[EMAIL PROTECTED]> wrote: Thomas

[gmx-users] topology of cyclohexane

Guys, Does anybody have an already prepared topology of cyclohexane? Thanks. -- Vitaly ___ 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 be

Re: [gmx-users] still system exploid

Morteza Khabiri wrote: Dear gmxuser, Thanks for your all helps. But still I have problem. As you friend said I increase the vdw and box size and also i decrease the time step till 0.0001 but unfortunately system crash befor EM running. I do check with ngmx. To reply the question that said what

[gmx-users] ligand parameterization for amber port in gmx

Dear people, I have parameterized a ligand with one phosphate and one pyrophospate group using antechamber with AM1-BCC charges and the GAFF forcefield. Amber files were converted to gmx files (*.itp/*.top and *.gro) with the amb2gmx conversion tool (http://www.alchemistry.org/wiki/index.php/Free_

Re: [gmx-users] simulation in vacuum

Thomas Schlesier wrote: >>/ Thank you. > />/ But i have one last question: > />/For epsilon_rf i use the relative permittivity of the medium. I simulate >in > />/vacuum so epsilon_rf would be 1? > /GROMOS ff is not parameterized for vaccum simulations of the b-something > version ... have

Re: [gmx-users] simulation in vacuum

Actually in vaccum the RF is meaningless ... use cutoff. On Wed, 17 Sep 2008 18:49:38 +0200 Thomas Schlesier <[EMAIL PROTECTED]> wrote: >>/ Thank you. > />/ But i have one last question: > />/For epsilon_rf i use the relative permittivity of the medium. I simulate in > /

Re: [gmx-users] sampling conformation on the basis of RMSD value

vivek sharma wrote: Hi There, I have a 5 nsec trajectory file for my system...and a RMSD plot for the same. while doing simulation I have sampled the frame at each 500 ps, Now I want to choose conformation on the basis of RMSD values, like conformation which has RMSD difference of some value

Re: [gmx-users] simulation in vacuum

>>/ Thank you. > />/ But i have one last question: > />/For epsilon_rf i use the relative permittivity of the medium. I simulate >in > />/vacuum so epsilon_rf would be 1? > /GROMOS ff is not parameterized for vaccum simulations of the b-something > version ... have look at the

Re: [gmx-users] simulation in vacuum

Xavier Periole wrote: On Wed, 17 Sep 2008 16:14:08 +0200 Thomas Schlesier <[EMAIL PROTECTED]> wrote: / Thank you. />/ But i have one last question: />/For epsilon_rf i use the relative permittivity of the medium. I simulate in />/vacuum so epsilon_rf would be 1? /GROMOS ff is not parameter

[gmx-users] g_dipoles index file

Hi, I am trying to calculate the N-H dipole autocorrelation function of my protein using g_dipoles. The mentioned the atom numbers of these two in my index file. I have given the following command: g_dipoles -f md_minim_traj.trr -s MD_1BA4.tpr -P 2 -corr mol -c dipo_corr.xvg -b -e 1000 -n

[gmx-users] Re: [Fwd: still system exploid]

Good file. I see no problems in it. However I asked not only for the gro file but also force field parameters. If you really need help the best variant to provide all the system you try to simulate. > > I could not send my file by gmx user because of this I attached it to email. > > Thanks for yo

Re: [gmx-users] About QH entropy, could you please help me?

(1) 6 eigenvalues represent rotation and translation. For (very) small molecules, these can be quite substantial, see Carlsson and Aqvist, /J. Phys. Chem. B,/ *109* (13), 6448 -6456, 2005. By fitting you remove the rotation and translation. You can search the literature for papers that discuss the

Re: [gmx-users] simulation in vacuum

On Wed, 17 Sep 2008 16:14:08 +0200 Thomas Schlesier <[EMAIL PROTECTED]> wrote: / Thank you. />/ But i have one last question: />/For epsilon_rf i use the relative permittivity of the medium. I simulate in />/vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulati

[gmx-users] simulation in vacuum

>/ Thank you. />/ But i have one last question: />/For epsilon_rf i use the relative permittivity of the medium. I simulate in />/vacuum so epsilon_rf would be 1? /GROMOS ff is not parameterized for vaccum simulations of the b-something version ... have look at the paper. So i should use ffG43b1

[gmx-users] sampling conformation on the basis of RMSD value

Hi There, I have a 5 nsec trajectory file for my system...and a RMSD plot for the same. while doing simulation I have sampled the frame at each 500 ps, Now I want to choose conformation on the basis of RMSD values, like conformation which has RMSD difference of some value say A nanometer. Can anybo

[gmx-users] About QH entropy, could you please help me?

Dear Li Yang, I forward your email to the GMX mailing list, which may be better for you since other users can contribute as well. I'll reply there - I hope you've subscribed to the list. Ran. Li Yang wrote: > Dear Ran Friedman > > I'm sorry to disturb you, my name is Li Yang, I'm a chinese student

Re: [gmx-users] Re: Change of force field: ffgmx > ff53a5

On Wed, 17 Sep 2008 15:00:17 +0200 Thomas Schlesier <[EMAIL PROTECTED]> wrote: Thank you. But i have one last question: For epsilon_rf i use the relative permittivity of the medium. I simulate in vacuum so epsilon_rf would be 1? GROMOS ff is not parameterized for vaccum simulations of the b-so

[gmx-users] Re: Change of force field: ffgmx > ff53a5

Thank you. But i have one last question: For epsilon_rf i use the relative permittivity of the medium. I simulate in vacuum so epsilon_rf would be 1? Thomas On Wed, 17 Sep 2008 14:27:57 +0200 Thomas Schlesier http://www.gromacs.org/mailman/listinfo/gmx-users>> wrote: >/ Ok, then i would take

Re: [gmx-users] Re: Change of force field: ffgmx > ff53a5

On Wed, 17 Sep 2008 14:27:57 +0200 Thomas Schlesier <[EMAIL PROTECTED]> wrote: Ok, then i would take to following parameters: _x is vdw or coulomb rlist 1.7 (must be greater then r_x) r_x1.4 r_x_switch0.8 x_typeshift right?!? No, rlist 0.8 nstlist 5 rcoulomb 1.4 rvdw 1.4 vdwty

[gmx-users] Re: Change of force field: ffgmx > ff53a5

Ok, then i would take to following parameters: _x is vdw or coulomb rlist 1.7 (must be greater then r_x) r_x1.4 r_x_switch0.8 x_typeshift right?!? Thomas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: Re: [gmx-users] Position restrain of protein and membrane

Thanks Justin for your reply, You mean to say that first keep PR on protein allowing the lipids to move(packing), later switch over to production run without keep PR on lipids? Here iam getting doubt that, While embedding protein into popc some of the lipids will be deleted led to creation of

[gmx-users] restarting REMD checkpoint gmx-cvs

Hi users, I would like to restart some REMD simulations done with the cvs code with the new checkpoint feature, but I'm unsure if I'm doing it right. Each replica has its own state#.cpt file, but it seems to me that the -cpi option of the cvs mdrun (at version 3.3.99_development_20080718) only a

Re: [gmx-users] PBS Script - trjconv Options

VENKATESH HARIHARAN wrote: Hello, Simple question. I am running constraint pulling and getting the .xtc and .tpr output files in order to create a pdb video using trjconv. I am running simulations on a cluster, and so a pbs script must be submitted with the necessary commands. When using

Re: [gmx-users] Change of force field: ffgmx > ff53a5

On Wed, 17 Sep 2008 11:56:41 +0200 Thomas Schlesier <[EMAIL PROTECTED]> wrote: Dear all, i have changed the topologie but i have a question regarding the following simulations. With ffgmx the length of the cut-offs (/rcoulomb /and /rvdw/) is standard 1.0 (default adjustment by GROMACS). I believ

[gmx-users] T-WHAM for replica

Hello everyone, Does anyone have a script to do T-WHAM analysis of replica exchange trajectories? Any help would be great! Thanks, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] Change of force field: ffgmx > ff53a5

Dear all, i have changed the topologie but i have a question regarding the following simulations. With ffgmx the length of the cut-offs (/rcoulomb /and /rvdw/) is standard 1.0 (default adjustment by GROMACS). I believe that i've seen some time ago that for the GROMOS96 force fields the cut-offs sho