Re: [gmx-users] [ pairs_nb ]

Robson da Silva wrote: Hi, What's the use of the directive [ pairs_nb ]? I don't find anything in the manual. It's not a directive I've ever seen or heard of. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] [ pairs_nb ]

Hi, What's the use of the directive [ pairs_nb ]? I don't find anything in the manual. Thanks. - Robson da Silva mail: roolib...@gmail.com ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

Re: [gmx-users] Water clustering

Hi Taka, I'd say you need to add some more water :) But in addition to that, you definitely should run with pressure coupling in stead of at constant volume. Cheers, Tsjerk 2009/7/10 H T : > Hi, I am trying to calculate micelle formation with SDS molecules for > all-atom simulation. > 49 SDS mo

Re: [gmx-users] global rmsf fraction to each eigenvector

Hi Fabricio, With total RMSF, do you mean over all atoms or total per atom? The former is simply the eigenvalue divided by the sum of all eigenvalues. For the latter, check g_anaeig. Cheers, Tsjerk On Fri, Jul 10, 2009 at 7:01 PM, Ragnarok sdf wrote: > Once I have the eigenvalue.xvg, how do I c

Re: [gmx-users] Can I change xtc-groups while continuing a simulation?

Hi Michael, > My only idea so far sounds pretty hacky: use the original coordinates and > mdp file to make a phony "initial.tpr" with the new xtc-groups and pass this > phony file on to tpbconv. I'm hesitant to do this because I don't actually > know what all is in a .tpr file and whether this wou

[gmx-users] global rmsf fraction to each eigenvector

Once I have the eigenvalue.xvg, how do I calculate the fraction of total RMSF that each eigenvector contributes, i.e., how do I find out that, for example, my first eigenvector is responsible for 73% of my total rmsf and so on. Thank you in advance Fabrício Bracht __

[gmx-users] Can I change xtc-groups while continuing a simulation?

Hi, I have a GROMACS 3.3.3 simulation that I'd like to extend. I can follow the instructions on the wiki ( http://oldwiki.gromacs.org/index.php/Extending_Simulations) to extend it, but I want to change the xtc-groups, and I'm not sure how to do that. I've looked at the help messages, looked at the

[gmx-users] Best way to handle linear rigid molecules.

Hello users, I am using gromacs v 4.0.5 What is the best way to treat linear triatomic molecules such as CO2. Is there some kind of rigid algorthym as in DL_POLY? In the asbsence of a ?rigid? algorthym. I initially intended to ?fix? the C=O bond length using constraints (as below) and some

[gmx-users] Water clustering

Hi, I am trying to calculate micelle formation with SDS molecules for all-atom simulation. 49 SDS monomers (will increase it later) were settled in 15nm x 15nm x 15nm box. And I put water molecules from spc216.gro to the box. Considering water density is 1g/ml, around 112800 molecules are require

Re: [gmx-users] Convert trr into crd (amber format)

I think that you can do it in vmd On Tue, Jul 7, 2009 at 11:18 PM, Ragnarok sdf wrote: > I came across a tool for making "porcupine" plots out of my PCA > analysis, but first I need to perform the analysis with a program that > accepts .cdr (amber traj) file format (the name of the program is >

Re: [gmx-users] Regarding numbering

Dear P.R.Anand Narayanan, > 1. how did the number of atoms and residues change. Hydrogen atoms were added to your structure, which accounts for the increase in number of atoms. The number of residues should not have changed. Probably there is a discrepancy between the number of residues you have

[gmx-users] Regarding numbering

Dear gromacs users, my protein has 4453 atoms and 583 residues. after running the pdb2gmx command it got converted to 5657 atoms and 581 residues. I cut and pasted the HETATMS from the initial pdb file into a separate file. My queries are: 1. how did the number of atoms and residues change. 2. wh