Re: [gmx-users] simulation with ligand at the active site

onetwo wrote: Hello Users, I have a query regarding simulation with the ligand. In my protein there are two ligands, one of them (coenzyme) is from the crystal data, and other I have docked at the active site, while docking it is showing good interaction with all the active site residues

Re: [gmx-users] rigid tetrahedral molecule

On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a

Re: [gmx-users] simulation with ligand at the active site

On 4/28/2011 3:21 PM, onetwo wrote: Hello Users, I have a query regarding simulation with the ligand. In my protein there are two ligands, one of them (coenzyme) is from the crystal data, and other I have docked at the active site, while docking it is showing good interaction with all the

Re: [gmx-users] Docking

Dear Aldo Thank you for your reply Mark's notes and yours were very useful. Best mohsen On Wed, Apr 27, 2011 at 6:46 PM, Aldo Segura asegurac...@yahoo.com.mxwrote: Before making a MD simulation you should try to explore different ways to analyze your docking results. For example, performing

[gmx-users] R: Md continuation with cpt

Dear Justin, thank you for your precious help. Yes, the problem is what you say and what I was suspecting too (but I was not sure, that's why I was searching for a confirmation of my suspects from more expert people). The problem however is present in the NVT-NPT junction. My .mdp settings were

[gmx-users] Fwd: Fwd: Need some assistence

Could someone assist me seeing as i am only a beginner at molecular dynamics i have generated models using modeller software and selected the best model based on DOPE GA341 and Prosa now i have performed energy minimisations using gromacs software. I further energy refined the structures

[gmx-users] Metal surfaces

Hello, does anybody have an idea if there are availbale PDB files which represent metal surfaces for transition state metals, to be used for MD? BW S -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] rigid tetrahedral molecule

Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of constraints ), we would have 4 bonds

[gmx-users] RE: Metal surfaces (Sergio Manzetti)

Hi, That's unlikely, but maybe the following publications can help you to build the surface: @Article{Iori2008, author = Iori, F and Corni, S, title = {Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces}, journal = J Comput Chem, year = 2008,

Re: [gmx-users] RE: Metal surfaces (Sergio Manzetti)

Thank you On Thu, Apr 28, 2011 at 6:26 PM, Ran Friedman ran.fried...@lnu.se wrote: Hi, That's unlikely, but maybe the following publications can help you to build the surface: @Article{Iori2008, author = Iori, F and Corni, S, title = {Including image charge effects in the molecular

Re: [gmx-users] rigid tetrahedral molecule

On 4/28/2011 7:07 PM, Sanku M wrote: Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of

Re: [gmx-users] rigid tetrahedral molecule

Sanku M wrote: Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of constraints ), we

Re: [gmx-users] Fwd: Fwd: Need some assistence

On 4/28/2011 6:10 PM, Ruben Cloete wrote: Could someone assist me seeing as i am only a beginner at molecular dynamics i have generated models using modeller software and selected the best model based on DOPE GA341 and Prosa now i have performed energy minimisations using gromacs software.

Re: [gmx-users] R: Md continuation with cpt

On 4/28/2011 5:47 PM, Anna Marabotti wrote: Dear Justin, thank you for your precious help. Yes, the problem is what you say and what I was suspecting too (but I was not sure, that's why I was searching for a confirmation of my suspects from more expert people). The problem however is present in

[gmx-users] pdb2gmx with input topology

Dear Gromacs users, I wish to convert PDB files to gromacs format while specifying the topology; however, in the pdb2gmx program, a .top file can only be an output, not an input. The need arises as I have an NMR PDB structure (including hydrogens) which I rather violently perturb into

Re: [gmx-users] pdb2gmx with input topology

Ehud Schreiber wrote: Dear Gromacs users, I wish to convert PDB files to gromacs format while specifying the topology; however, in the pdb2gmx program, a .top file can only be an output, not an input. The need arises as I have an NMR PDB structure (including hydrogens) which I rather

Re: [gmx-users] pdb2gmx with input topology

On 4/28/2011 10:25 PM, Justin A. Lemkul wrote: Ehud Schreiber wrote: Dear Gromacs users, I wish to convert PDB files to gromacs format while specifying the topology; That is not the role of pdb2gmx. pdb2gmx generates a topology that matches a configuration (which could be in one of

[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

Dear gmx users, Recently I have parametrized a new force field for glycolipid molecules based on the GLYCAM parameters. I would like to use it with the AMBER99SB-ILDN force field in gromacs for simulations of peptides and glycolipds. As you know GLYCAM uses two different values for fudgeLJ

Re: [gmx-users] simulation with ligand at the active site

Previously, something like happened to me, the solution that worked for me was to use acpype (code.google.com/p/acpype) and Amber FF. In this way, you could rule out problems related to the prodrg parameters. Best regards, Aldo === Aldo Segura-Cabrera

[gmx-users] Benchmarking gromacs over large number of cores

Hi, I'm not really a Gromacs user, but I'm currently benchmarking Gromacs 4.5.4 on a large cluster. It seems that my communication (PME) is really high and gromacs keeps complaining for more PME nodes : Average load imbalance: 113.6 % Part of the total run time spent waiting due

[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

Stephane: The problem is the coulombic 1-4 interactions. There is not (and never has been as far as I can tell) a way to get different 1-4 coulombic scaling for different pairs. There is a trick that works when combining one ff that uses fudgeQQ 1.0 and another that uses fudgeQQ 0.5:

[gmx-users] R: Md continuation with cpt

Dear Mark, thank you very much for your hint. It's a relief to know that I haven't to redo the simulation! From now on I will set init_step = 0 for my simulations. Anna -- Message: 3 Date: Thu, 28 Apr 2011 20:56:00 +1000 From: Mark Abraham mark.abra...@anu.edu.au

[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

Aargh !! it is not easy :(((, I will try, your trick, Chris. By the way, thank your for pointing the paper. A bientot Stéphane Message: 5 Date: Thu, 28 Apr 2011 10:45:17 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Use different fudgeLJ and fudgeQQ values in

Re: [gmx-users] Benchmarking gromacs over large number of cores

how many particles is your system? if the number per domain is too low there is not much you can do about the load imbalance...but it did report only an overall 3.2% overhead for this so... you can modify the PP/PME ratio during mdrun by manually specifying the domain decomposition yourself.

[gmx-users] ordering components of system using trjorder

Dear gmx-users, I wish to order the components of my system with respect to the polypeptide using trjorder. I want to select my first group as the protein and the second group to be ordered is non-protein (i.e all other components in the system except polypeptide) the command I am using is:

[gmx-users] Re: gmx-users Digest, Vol 84, Issue 217

Hi Ivan If in my system there are some of the other components such SDS surfactant and one of these polarizable models can I use forcefield parameters from PRODRG or not. If no, would you please tell me about the references that I can find some other components in polarizable water model force

[gmx-users] trjorder not working

Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water

Re: [gmx-users] Benchmarking gromacs over large number of cores

On Thu, Apr 28, 2011 at 10:05 AM, Bruno Monnet bruno.mon...@hp.com wrote: Hi, I'm not really a Gromacs user, but I'm currently benchmarking Gromacs 4.5.4 on a large cluster. It seems that my communication (PME) is really high and gromacs keeps complaining for more PME nodes : Average

[gmx-users] how to get higher precision values for g_velacc

Dear gmx users, I am using g_velacc to calculate the velocity auto correlation. The output I am getting in .xvg file is much lower precision than I require. Is there a way to get the values in higher precision? Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] vdw cutoff options for opls forcefield

Hi, I was wondering whether someone can comment on what vdw-cutoff scheme will be suitable when using a molecule under OPLS/AA force field . Also, providing some details about what cut-off value one should use will be really helpful. Thanks Sanku-- gmx-users mailing list

[gmx-users] Turning OFF/ON distance restraints during a simulation

Hi all, Is it possible to turn OFF/ON distance restraints after simulating a system for a certain period of time? If yes, how do I command GMX to do such a job? Thank you James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing list

Re: [gmx-users] Turning OFF/ON distance restraints during a simulation

On 4/29/2011 9:09 AM, jayant james wrote: Hi all, Is it possible to turn OFF/ON distance restraints after simulating a system for a certain period of time? If yes, how do I command GMX to do such a job? You can do this only by stopping the simulation and re-invoking grompp with the changed

Re: [gmx-users] vdw cutoff options for opls forcefield

On 4/29/2011 8:28 AM, Sanku M wrote: Hi, I was wondering whether someone can comment on what vdw-cutoff scheme will be suitable when using a molecule under OPLS/AA force field . Also, providing some details about what cut-off value one should use will be really helpful. Generally, one

Re: [gmx-users] how to get higher precision values for g_velacc

On 4/29/2011 4:48 AM, shivangi nangia wrote: Dear gmx users, I am using g_velacc to calculate the velocity auto correlation. The output I am getting in .xvg file is much lower precision than I require. Is there a way to get the values in higher precision? Depends what you've done so far,

Re: [gmx-users] trjorder not working

On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and

Re: [gmx-users] how to get higher precision values for g_velacc

I want the velocity autocorrelation output in double precision. How can I get that? Thanks, SN --- On Thu, 4/28/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] how to get higher precision values for g_velacc To: Discussion

Re: [gmx-users] how to get higher precision values for g_velacc

On 4/29/2011 10:34 AM, shikha nangia wrote: I want the velocity autocorrelation output in double precision. How can I get that? Install GROMACS in double precision. Depending what the problem is, you might be able to run the double-precision g_velacc on the old data to get more precision,

Re: [gmx-users] trjorder not working

Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the

Re: [gmx-users] trjorder not working

On 4/29/2011 11:29 AM, shivangi nangia wrote: Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a