[gmx-users] How to control and interpret g_density analysis more precisely?

Dear Alex: be careful with g_density! If you do not use the symmetrize -symm option, then the box height is going to be taken as a single frame. If you do NpT, then you will get an incorrect (or at least noisy) result. I forget if this will bite you if you do use the -symm option. This is

Re: [gmx-users] How to control and interpret g_density analysis more precisely?

Alex Matyushov wrote: Thanks. Do you mean the "-d" option? What exactly does it mean by "take Yep, that's the one. the normal on the membrane"? What membrane? What if I was simulating a system that doesn't have any membranes? The g_density tool only really makes sense for interfacial-ty

Re: [gmx-users] How to control and interpret g_density analysis more precisely?

Thanks. Do you mean the "-d" option? What exactly does it mean by "take the normal on the membrane"? What membrane? What if I was simulating a system that doesn't have any membranes? Thank you, Alex On Fri, Aug 27, 2010 at 5:55 PM, Justin A. Lemkul wrote: > > > Alex Matyushov wrote: > >> Dear

Re: [gmx-users] How to control and interpret g_density analysis more precisely?

Alex Matyushov wrote: Dear Gromacs community, I've been using g_density to analyze distribution of atoms in an elongated box with a lipid bilayer and lipid monolayers at each end of the box. My results suggest that it found the density along the z-coordinate, which is the longest dimension

[gmx-users] How to control and interpret g_density analysis more precisely?

Dear Gromacs community, I've been using g_density to analyze distribution of atoms in an elongated box with a lipid bilayer and lipid monolayers at each end of the box. My results suggest that it found the density along the z-coordinate, which is the longest dimension in the box. That is indeed wh

Re: [gmx-users] Help on data anaysis in g_rdf and g_dist

tekle...@ualberta.ca wrote: Dear Justine, As for the distance, have you corrected for PBC? Are you analyzing the molecules that you think you are? No, I did not correct for the PBC. How can I do that. And what is the purpose of that in the g_dist calculation. Usually one uses trjconv. I

Re: [gmx-users] Help on data anaysis in g_rdf and g_dist

Dear Justine, As for the distance, have you corrected for PBC? Are you analyzing the molecules that you think you are? No, I did not correct for the PBC. How can I do that. And what is the purpose of that in the g_dist calculation. Yes, I just look at the last frame of my simulation and

Re: [gmx-users] Flat energy profile in g_wham

alexander yakovenko wrote: Hi all! there is a question about g_wham from gmx 4.0.5. I am integrating trajectory of dissociation of protein-DNA complex. All goes well but PMF profile from g_wham looks as straight line. Double check of pullf and pullx files showed that mdrun worked properly

[gmx-users] Flat energy profile in g_wham

Hi all! there is a question about g_wham from gmx 4.0.5. I am integrating trajectory of dissociation of protein-DNA complex. All goes well but PMF profile from g_wham looks as straight  line. Double check of pullf and pullx files showed that mdrun worked properly, forces are OK and reasonably

Re: [gmx-users] Help on data anaysis in g_rdf and g_dist

tekle...@ualberta.ca wrote: Dear Gmx users, After working for quite sometime I managed to simulated almost all my molecules for 20ns. Thank you for all your help especially Justine.Now I am on last stage of analyzing my data. First: I want to calculate g(r)and I used the following command

Re: [gmx-users] Help on data anaysis in g_rdf and g_dist

Dear Gmx users, After working for quite sometime I managed to simulated almost all my molecules for 20ns. Thank you for all your help especially Justine.Now I am on last stage of analyzing my data. First: I want to calculate g(r)and I used the following command g_rdf -f PAP_20ns.xtc -s PA

[gmx-users] The last beta release: Gromacs-4.5-beta4

The last beta release of Gromacs-4.5-beta4 is available for download. The AMBER FF have been validated and are now production ready; the GPU code had a serious bug fixed, and there is a new tool g_pme_error (it will be incorporated in g_tune_pme soon though). Most of the critical issues sinc

Re: [gmx-users] drude oscillator with thole polarization

On 2010-08-27 18.14, k...@chem.wisc.edu wrote: Hello gmx-users, I am trying to implement a Drude oscillator model with Thole polarization in Gromacs 4.0.5. As the manual stated, it is implemented in Gromacs, but no further instructions can be found in manual. An example of water ( sw.itp ) can b

[gmx-users] drude oscillator with thole polarization

Hello gmx-users, I am trying to implement a Drude oscillator model with Thole polarization in Gromacs 4.0.5. As the manual stated, it is implemented in Gromacs, but no further instructions can be found in manual. An example of water ( sw.itp ) can be found, but there is no thole polarizat

[gmx-users] NPT simulation

Dear Dr.Chaban, Thanks for your message. Now I have to groups: PE is a single chain and HEX (343 hexane molecules). I am interested in nonbonded interaction energies between PE and solvent as well as between PE-PE and HEX -HEX. I ran the simulation for 300ps and the system is equilibrating (300K

[gmx-users] Re: NPT simulation

Dear Moeed: 1. Please note, this is Justin here who likes long descriptions but I like those which are as short as possible. :-) Please formulate your questions more specifically because I am too lazy (and busy unfortunately) to read all your MD novels at ones. 2. If I said that the energy was gi

[gmx-users] Saving velocities

Hi, Does anybody knows how to save the velocities of a group of particles every N time steps without having to write the .trr file for the whole system? I mean my system has two kinds of molecules say A and water what I want is to save the velocities for the atoms in the molecule A every certain n

[gmx-users] 3D solvent density distribution

Hi all, I would like to extract a 3D density distribution for particular species from simulations (not z averaged or slices). My feeling is that g_sdf or g_spatial (v. 4.0.5 ) should be able to do this - the gaussian cube format would be ideal output for me - but I've not managed to fully un

[gmx-users] CHARMM lipids

Hi Yuanyuan, I send a copy of this discussion to gmx-users. We can continue the discussion there so other users can benefit from it. 27 aug 2010 kl. 09.27 skrev yuanyuan3201003: > Dear professor, > Thanks for your reply , but the lipid parameter in gromacs 4.5 beta2 is not > including DPPC,D

[gmx-users] Internal Density

Dear all, I have 2 structures similar to a Beta-turn where the inside is hydrophobic, and I would like to find the density of just this part of the strucuture. More specifically, both structure are identical expect for one mutation. One of the structures contains 2 glycines facing each other

Re: [gmx-users] Please solve this

Pawan, What are you trying to do? Tsjerk On Fri, Aug 27, 2010 at 9:16 AM, pawan raghav wrote: > I am posting this question second time so please tell me, where I was wrong? > > In manual g_analyze reads an ascii file and analyzes data sets, in which > input file was graph.xvg. To generate eigen

[gmx-users] contact residues

I have used g_mdmat g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg I got dm.xpm graph which shows mean of whole simulation residue contacts. How to get information about the particular residue are in contact? how to get list of contact residues? In graph file num.xvg there

[gmx-users] Please solve this

I am posting this question second time so please tell me, where I was wrong? In manual g_analyze reads an ascii file and analyzes data sets, in which input file was graph.xvg. To generate eigenvector and eigenvalue file I have used g_covar and analyzed eigenvectors by g_aneig. So according to manu

[gmx-users] g_anaeig

Thankyou so much Tsjerk Wassenaar -- Pawan -- 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. Use the www interfac