[gmx-users] spc vs. flex_spc

Dear gmx-users, I am wondering whether or not there is a good reason to use flex_spc during energy minimisation and spc during production run? I guess one would not use flex_spc during a production run as this would decrease the time step needed quite a lot - but is it a good idea to use durin

RE: [gmx-users] spc vs. flex_spc

Hi, flex_spc is not a reliable water model, never use it for MD. You should only use it when your initial configuration is so bad that energy minimization with normal, rigid water molecules crashes. However, the deviations are so small that after a few picoseconds of MD with normal spc there will

SV: [gmx-users] spc vs. flex_spc

Thank you very much for your quick answer Berk! Fra: gmx-users-boun...@gromacs.org på vegne af Berk Hess Sendt: ma 15-02-2010 10:56 Til: Discussion list for GROMACS users Emne: RE: [gmx-users] spc vs. flex_spc Hi, flex_spc is not a reliable water model, never u

[gmx-users] problem with the translate option of editconf

Hi all, I am trying to translate the peptide within the simulation box. I have a box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the peptide on top of the box. In order to that I used the following command line: editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0 0 1.5 -o trans.pdb The

Re: [gmx-users] problem with the translate option of editconf

Ozge Engin wrote: Hi all, I am trying to translate the peptide within the simulation box. I have a box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the peptide on top of the box. In order to that I used the following command line: editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0

Re: [gmx-users] problem with the translate option of editconf

Ozge Engin skrev: Hi all, I am trying to translate the peptide within the simulation box. I have a box with dimensions of 3.8 3.0 3.0 nm^3, and I want to put the peptide on top of the box. In order to that I used the following command line: editconf -f pep.pdb -box 3.8 3.0 3.0 -translate 0

[gmx-users] Poor load balancing

Hi All, I'm trying to d.lzm gromacs benchmarks with 64 node machine, but dynamic load balancing performance is very low. Any suggestion will be of great help. Thanks. Deniz KARASU Log file opened on Sat Feb 13 17:23:37 2010 Host: d077.uybhm.itu.edu.tr pid: 20157 nodeid: 0 nnodes: 64 The

[gmx-users] pbc whole

Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj Before, I had a problem with residues of my protein showing at the other end

Re: [gmx-users] pbc whole

Carla Jamous wrote: Hi everyone, I'm using this command to extract my protein and my ligand from the trajectory. trjconv -f prot_md60ns.xtc -s prot_md50.tpr -fit rot+trans -pbc whole -n prot_wat.ndx -o prot_ligand_60ns.xtc < grps >& outtrj Before, I had a problem with residues of my prote

Re: [gmx-users] Poor load balancing

Hi, 18 seconds real time is a bit short for such a test. You should run at least several minutes. The performance you can expect depends a lot on the interconnect you are using. You will definitely need a really low-latency interconnect if you have less then 1000 atoms per core. Carsten On Fe

[gmx-users] How to select the molecules within a defined radius

Hi all, I am doing some simulations in binary solvent water and DMSO using ffG43a6 forcefield. I need to calculate the composition fluctuation of the solvent. I have done that with hand-written codes using the trajectory files generated by GROMACS. I selected a sphere at a fixed center and noted t

Re: [gmx-users] How to select the molecules within a defined radius

Saikat Banerjee wrote: Hi all, I am doing some simulations in binary solvent water and DMSO using ffG43a6 forcefield. I need to calculate the composition fluctuation of the solvent. I have done that with hand-written codes using the trajectory files generated by GROMACS. I selected a sphere

Re: [gmx-users] Problems wtih g_wham

Thank you so much! I appreciate the help, and the good news is actually great news. Jenny On Sun, Feb 14, 2010 at 12:45 PM, Jochen Hub wrote: > Jennifer Casey wrote: > >> Hello, >> >> I am trying to create a PMF for the sodium cation and iodine anion in the >> presence of THF. I have been fol

[gmx-users] number of adsorbed gas+silicon nanotube

Hi , please answer my questions 1- for performed (MD) simulation to study adsorption gas on silicon nanotube  ,I used from  g_rdf and trjorder programs ,how I can measure adsorption coverage (number of adsorbed gas)on surface of the nanotube ? 2-while running g_msd program ,in the option select

[gmx-users] (no subject)

What is coordination number and which  program generate  it? -- 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 l

Re: [gmx-users] How to select the molecules within a defined radius

> > > Saikat Banerjee wrote: >> I am doing some simulations in binary solvent water and DMSO using ffG43a6 >> forcefield. I need to calculate the composition fluctuation of the solvent. >> I have done that with hand-written codes using the trajectory files >> generated by GROMACS. I selected a sp

[gmx-users] pbc with nwall = 1

Hello, I want to study polymer adsorption onto a surface. To do so, I create a polymer-solvent system with a wall at z = 0 and use pbc = xy. This, however makes the system infinite in the z-direction. I was wondering if there was a way to create a periodic boundary at z = L such that when a

Re: [gmx-users] How to select the molecules within a defined radius

Hi, On Mon, Feb 15, 2010 at 19:04, Saikat Banerjee wrote: > I selected a sphere at a fixed center and noted the > number of water and DMSO molecules within that cut-off. I would like to know > if there are any methods to do the same within GROMACS. The development (git) version of Gromacs has fo

Re: [gmx-users] number of adsorbed gas+silicon nanotube

Turtle Nedasing wrote: Hi , please answer my questions 1- for performed (MD) simulation to study adsorption gas on silicon nanotube ,I used from g_rdf and trjorder programs ,how I can measure adsorption coverage (number of adsorbed gas)on surface of the nanotube ? Using g_dist -dist migh

Re: [gmx-users] (no subject)

Turtle Nedasing wrote: What is coordination number and which program generate it? That depends on your context, and there probably isn't a Gromacs program that generates it magically, but with a combination of tools to describe whatever criteria you're assigning, you might be able to ge

[gmx-users] pbc option

Hi Everyone, I changed the gromacs source code a little bit and this change introduced some bias along x direction. Now i want to do a 'yz' pbc but gromacs has the option of pbc = xy only. Is there a quick tip to circumvent? I can always introduce the bias along z but its a little time taking job

Re: [gmx-users] pbc option

On 02/16/10, Amit Choubey wrote:Hi Everyone,I changed the gromacs source code a little bit and this change introduced some bias along x direction. Now i want to do a 'yz' pbc but gromacs has the option of pbc = xy only. Is there a quick tip to circumvent? I can always introduce the bias along z b

[gmx-users] indexing and new molecules

Shalom all, I am simulating a protein in which one of the residues is chemically modified (non-natural) - so I had to add it into aminoacids.dat. I found that when I analyse my results, and use the index group of the protein this amino acid does not count unless the aminoacids.dat file is availab

Re: [gmx-users] indexing and new molecules

On 02/16/10, Itamar Kass wrote:Shalom all,I am simulating a protein in which one of the residues is chemicallymodified (non-natural) - so I had to add it into aminoacids.dat.I found that when I analyse my results, and use the index group of theprotein this amino acid does not count unless the ami

Re: [gmx-users] indexing and new molecules

Hi Mark, Thanks for the replay. I actually hold the modified force filed files in the same directory in which I simulate, less mess in the system. Cheers, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =

[gmx-users] Analysis of a simulation

Dear All, It is not clear from manual how to analyse my requirements after simulation. Could you please help me in the following regards: 1> How to get the graph on "occupancy of hydrogen bond interactions of ligands throughout 5 ns simulation" and "occupancy of a particular salt-bridge throug