[gmx-users] Seperation of specific trajectory from whole trajectory file.

Hi all, I have run the protein simulation for 7ns with time interval 1ns each time, after that I catenated all the trj files by using trjcat command. Now I want to separate the 1ns .xtc from 7ns trajectory, is it possible to recover the 1ns trajectory file from entire 7ns trajecto

Re: [gmx-users] 2D projection and corresponding conformation

xi zhao wrote: > Dear user: > We know that observing the sampled conformations in the subspace spanned > by the eigenvectors is a so-called two-dimensional projection(2D > projection), in 2-D projection, each point represents a snapshot from > the simulation, and the distribution shows the sampl

[gmx-users] 2D projection and corresponding conformation

Dear user: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along the fir

[gmx-users] Simulating Protein+Dextran/PEG

Dear All, I am a newbie to GROMACS and to MD simulations. I want to simulate and study protein in the presence of Dextran or PEG. 1. From literature and internet searches, I understand that PEG topology file can be generated using the PRODRG server and hence protein+PEG simulations should be possi

Re: [gmx-users] Nitrogen Flow over cylinder

Andy Shelley wrote: I am trying to simulate the flow of nitrogen over a cylinder and would like to use gromacs. Most of the simulations seem to be done in water, but I was wondering how to go about creating the simulation in Nitrogen. I can create the cylinder. After that I want to try to crea

[gmx-users] Nitrogen Flow over cylinder

I am trying to simulate the flow of nitrogen over a cylinder and would like to use gromacs. Most of the simulations seem to be done in water, but I was wondering how to go about creating the simulation in Nitrogen. I can create the cylinder. After that I want to try to create a shear flow by assig

Re: [gmx-users] simulating Ubiquitinated protein

AJIT DATTA wrote: Hi I am trying to do MD simulation of a ubiquitinated protein. (C-terminal linked to a lysine residue via an isopeptide bond). But I am not being able to define the isopeptide link. can someone help me out in this? Ajit B. ___ gmx-u

[gmx-users] simulating Ubiquitinated protein

Hi I am trying to do MD simulation of a ubiquitinated protein. (C-terminal linked to a lysine residue via an isopeptide bond). But I am not being able to define the isopeptide link. can someone help me out in this? Ajit B. ___ gmx-users mailing list

Re: [gmx-users] how to distancing the counter ions from the protein?

jayant james wrote: well it seems to be on the protein's surface is it OK? What command did you issue? Random placement of ions can sometimes lead to ions being placed in unhappy places, in which case you can just run genion again with a different random seed. If you told genion to place

Re: [gmx-users] still problems with dodecahedron box and editconf

Maybe trjconv -ur compact could help you... Cheers, Jochen Sebastian Kruggel wrote: Dear gmx-er, I have problems creating (or visualizing) a dodecahedron box. I found simular problems in the mailing list, where running mdrun is supposed to help - but this does't work in my case. I gener

Re: [gmx-users] how to distancing the counter ions from the protein?

well it seems to be on the protein's surface is it OK? On Mon, Jun 9, 2008 at 6:08 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > jayant james wrote: > >> Hi! >> I had to incorporate a salt conc of 0.15M NaCl and once I have them in put >> in the the box,via genion, I find that they are in close p

Re: [gmx-users] analysis of different groups with g_energy

On Tuesday 10 June 2008 16:07, Mark Abraham wrote: > Peyman Yamin wrote: > > Good day! > > > > Thanks for the comments, but maybe it could be done in a less laborious > > way as following? > > > > g_energy gives all the interactions between MOL and SOL other than > > bonding ones. since there is no

Re: [gmx-users] genconf problem

ANINDITA GAYEN wrote: Dear all, I have download a POPG(lip 128+Na ion 128) bilayer from "http://www.softsimu.org/downloads.shtml";. I want to make a bilayer containing 128 lip/leaflate i.e, with 256 lipids having suqre surface area (X=Y). With the following commands : 1)"genconf -f popg.pdb

Re: [gmx-users] analysis of different groups with g_energy

Peyman Yamin wrote: Good day! Thanks for the comments, but maybe it could be done in a less laborious way as following? g_energy gives all the interactions between MOL and SOL other than bonding ones. since there is no bond between MOL and SOL, one could do a ONE step simulation of MOL with

Re: [gmx-users] g_density problem segmentation fault glibc detected

Here are the answers to the questions: Did see the trajectory. Looks fine Did start from different initial time frames, and thicker slabs, problem does not go away Yes, the simulation has run for ~ 80 ns. It is equilibrated Which log file ? What I reported was from the log file On Tue, Jun 10

Re: [gmx-users] secondary structure

s lal badshah wrote: Hi All, I want to study and calculate the secondary structure as a function of time of my MD simulated protein. I have no DSSP installed but will use VMD for this.Can any one suggest me which files of MD simulation output I should used? or I need to develop PDB file of the

Re: [gmx-users] secondary structure

s lal badshah wrote: Hi All, I want to study and calculate the secondary structure as a function of time of my MD simulated protein. I have no DSSP installed but will use VMD for this.Can any one suggest me which files of MD simulation output I should used? or I need to develop PDB file of t

Re: [gmx-users] g_density problem segmentation fault glibc detected

Have you seen the trajectory? Did you try to start from different frames? Is your system equilibrated? check log file! Peyman On Tuesday 10 June 2008 13:35, himanshu khandelia wrote: > Hi, > > I am trying to calculate the density in a bilayer simulation: > > echo 27 | g_density -f lipiddrg.xt

Re: [gmx-users] secondary structure

At best use all those you need! Also the manual could help, so could google.com as well as the university library. Be well On Tuesday 10 June 2008 12:53, s lal badshah wrote: > Hi All, > I want to study and calculate the secondary structure as a function of time > of my MD simulated protein. I

[gmx-users] g_density problem segmentation fault glibc detected

Hi, I am trying to calculate the density in a bilayer simulation: echo 27 | g_density -f lipiddrg.xtc -n all.ndx -s all.tpr -o head.xvg -sl 200 -b 4 The system size is about 6.5 x 6.5 x 9.6 I get the following error, after g_density has read most of the trajectory: *** glibc detected *** g

[gmx-users] genconf problem

Dear all, I have download a POPG(lip 128+Na ion 128) bilayer from "http://www.softsimu.org/downloads.shtml";. I want to make a bilayer containing 128 lip/leaflate i.e, with 256 lipids having suqre surface area (X=Y). With the following commands : 1)"genconf -f popg.pdb -nbox 2 2 1 -dist 0 0 0 -

Re: [gmx-users] TEE-REX installation error

Thanks for the answer, configuring with --enable-mpi solves the problem. Just to note it was not totally clear from the TEE-REX documentation that this had to be the case, however suppose i should have thought about it and realised replica exchange is usually ran on more than one processor! T

[gmx-users] secondary structure

Hi All, I want to study and calculate the secondary structure as a function of time of my MD simulated protein. I have no DSSP installed but will use VMD for this.Can any one suggest me which files of MD simulation output I should used? or I need to develop PDB file of the whole MD simulation tr

RE: [gmx-users] Possible issues with CVS pull code 200800508

Dear Berk, Yes, I use the walls only to allow efficient neighboursearch and to be able to utilize PME. You state that I pressure-couple in z, although I have put pcoupl=no and commented out the rest of the p-coupling parameters by initial semicolons in these lines. Have you changed the comme

Re: [gmx-users] analysis of different groups with g_energy

Good day! Thanks for the comments, but maybe it could be done in a less laborious way as following? g_energy gives all the interactions between MOL and SOL other than bonding ones. since there is no bond between MOL and SOL, one could do a ONE step simulation of MOL with its last acquired stru

[gmx-users] still problems with dodecahedron box and editconf

Dear gmx-er,   I have problems creating (or visualizing) a dodecahedron box. I found simular problems in the mailing list, where running mdrun is supposed to help - but this does't work in my case. I generated my box with the following commands   > pdb2gmx -f $PROT.pdb -o $PROT.gro -p $PROT.top -f