Re: [gmx-users] MnO2 periodic system

What do you mean "deformed"? The "deformation" that you have encountered is probably most likely due to the topology, rather than the simulation settings (since you have constant volume set). So that means there are issues with your topology. Catch ya, Dr. Dallas Warren Drug Delivery,

Re: [gmx-users] [gmx-developers] importing amber parameters to gromacs format?

On 8/7/17 2:47 PM, Ming wrote: Hi gromacs team, I am trying to simulate a protein ligand complex using gromacs, where I have two manganese ions bound with the ligand. I searched the gromacs force field and there was no parameter data for Mn. After some research online I found the

Re: [gmx-users] (no subject)

I did not quite understand your comment. However, I am trying my best to answer it. I have a surface MnO2 model. I have solvated the structure in all 3 directions. After that, I minimize it and run NVT simulation with the parameters as mentioned. However, I see that there is a deformation of

Re: [gmx-users] Memory issues using -ac option of gmx hbond

Hi, To diagnose such issues, explore using fewer frames and more restrictive selections for the analysis. Mark On Mon, 7 Aug 2017 23:55 Smith, Micholas D. wrote: > I had a similar problem. Using gromacs 2016.3's hbond tool fixed this. > > > === > Micholas

Re: [gmx-users] (no subject)

Hi, On the information given, nobody can tell whether the parameters you have for the interactions between Mn and O and maybe water are unsuitable, or that something is wrong with the method, or the initial conditions, or the code. Mark On Mon, 7 Aug 2017 23:11 gangotri dey

[gmx-users] Memory issues using -ac option of gmx hbond

I'm trying to analyzing hydrogen bonds between a DNA and protein complex. When using the -ac option of gmx hbond, I'm getting segmentation faults which look like an out-of-memory problem. However, I'm giving the process 64gb of memory, and an additional 64gb of virtual memory. How memory

Re: [gmx-users] (no subject)

I did not quite understand your comment. However, I am trying my best to answer it. I have a surface MnO2 model. I have solvated the structure in all 3 directions. After that, I minimize it and run NVT simulation with the parameters as mentioned. However, I see that there is a deformation of the

Re: [gmx-users] time calculations

Hi, I can't tell what question you're asking. Can you rephrase it please? Mark On Mon, 7 Aug 2017 08:05 faru honey wrote: > Please any one tell me that on what basis the time calculations occurs > that is in pico seconds > > > Sent from Mail for Windows 10 > > -- >

Re: [gmx-users] (no subject)

Hi, Are you trying to implement a model that you know is capable of produce a surface that does not deform in unexpected ways? Mark On Mon, 7 Aug 2017 16:35 gangotri dey wrote: > Dear all, > > I am trying to equilibrate a MnO2 surface (not cluster but periodic). I > have

Re: [gmx-users] solvate only in the z-direction

Solvate everything and then delete all molecules that have any inappropriate z coordinate. Or make a box whose lowest z coordinate is what you want, solvate that, and then add your surface below that. Mark On Mon, 7 Aug 2017 22:33 gangotri dey wrote: > Dear all, > > I am

Re: [gmx-users] clayff forcefield

Hi, Didn't someone already answer that you need to make a forcefield folder, eg in your working directory? You will need to follow the examples in the gromacs version you are using to name things appropriately. Mark On Mon, 7 Aug 2017 22:54 G R wrote: > Dear usres, > >

[gmx-users] clayff forcefield

Dear usres, I try to write clayff forcefield, and I want to simulate Kaolinite. I have some questions about it. 1) should I write clayff forcefield separately or modify one of the forcefields in share/top? 2) The directory for clayff forcefield should be included ffbonded.itp, ffnonbonded.itp,

[gmx-users] solvate only in the z-direction

Dear all, I am working with MnO2 surface and I would like to solvate the surface only in the z-direction. How best can I do it, please? *Thank you* *Gangotri Dey* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation

Thank you for your response. I did not have tabulated potentials for bonded interactions. I had tabulated potentials only for non-bonded interactions. I had set constraints to be all-angles in my mdp file. I will try using "constraint" interaction explicitly in my topology instead of converting

Re: [gmx-users] Non Standard residues moving Away

On 8/7/17 3:01 PM, Souvik Dey wrote: Hi, Grompp is running successfully without any errors. But my protein and ligands are very far away from each other. So, what I fear is that the interactions among them may not be well accounted for by MD simulations. If the coordinates that came out of

Re: [gmx-users] Non Standard residues moving Away

Hi, Grompp is running successfully without any errors. But my protein and ligands are very far away from each other. So, what I fear is that the interactions among them may not be well accounted for by MD simulations. On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham wrote:

Re: [gmx-users] Constraining starting configuration in Coarse-Grain Simulation

Hi, Tabulated bonded interactions are the opposite of constraints. You can explicitly use a "constraint" interaction type in your topology, which sounds like a good start. See chapter five of the reference manual. Mark On Mon, 7 Aug 2017 01:24 Maghesree Chakraborty

Re: [gmx-users] How to Identify clusters

Hi, The gromacs documentation pages list all the analysis programs available, along with a summary of what they can do. Each tool has its own documentation, too. Exploring that will tend to get you a useful answer sooner than emailing! Or at least a more focussed question. Mark On Sun, 6 Aug

Re: [gmx-users] Non Standard residues moving Away

Hi, The only thing that matters is the order of the molecules, residues and atoms, and preferably naming. These must match between topology and coordinates when you eg use grompp. The point of doing an MD simulation is generally to keep the topology constant while changing the coordinates. So

Re: [gmx-users] converting xtc to pdb without need to tpr file using trjconv

Thanks a lot Justin Neda - Original Message - From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Mon, 07 Aug 2017 19:08:05 +0430 (IRDT) Subject: Re: [gmx-users] converting xtc to pdb without need to tpr file using trjconv On 8/7/17 2:42 AM, Neda Rafiee wrote: >

Re: [gmx-users] Performance values

Szilárd, Thank you so very much for the reply!You mention that time/step is important if trying to do an apples-to-apples comparison for any given simulation. I have a few questions - For specific example, use the RNAse reference here: (http://www.gromacs.org/gpu )

Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

Dear Yujie Liu, Can I clarify your suggestions? copy gly.gro into protein.gro and changed the number of atoms: ) After running "gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o protein_glycine.gro", the "protein_glycine.gro" already contains both protein residues and glycine

Re: [gmx-users] converting xtc to pdb without need to tpr file using trjconv

On 8/7/17 2:42 AM, Neda Rafiee wrote: Dear users, Anyone knows how can I use trjconv to convert an xtc file to pdb format without need to tpr file ? trjconv does accept PDB files to -s but then you don't get PBC or connectivity information. You need to provide some source of atom and

Re: [gmx-users] trans-membrane protein simulation

On 8/6/17 10:25 PM, Amir Zeb wrote: Hello gmx-users! I want to simulate a membrane protein, where it sets across the membrane (means that some of the protein's region lays outside the membrane and is water exposed). Obviously, the protein will be experiencing two different environments like

Re: [gmx-users] Generating topology file for a long polymer chain

On 8/6/17 8:35 PM, Mahsa E wrote: Hello Justin, Thank you so much for your reply! I followed what you suggested. Please correct me if I misunderstood; 1- I used acpype to generate the parameters (charges, atom types, and bonded parameters) for the monomer, which create many files including

[gmx-users] (no subject)

Dear all, I am trying to equilibrate a MnO2 surface (not cluster but periodic). I have solvated the surface with water in all 3 directions. After the NVT run, I see that the surface is deformed. I was wondering what else can I add in my nvt.mdp to not encounter this problem? I have mainly

Re: [gmx-users] Gmx hbond

On 8/6/17 4:21 PM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi justin Thank you for your replyingBut you said in this tuturial, in order to

Re: [gmx-users] The small organic molecule occurred deformation during simulation

On 8/5/17 2:59 PM, yujie liu wrote: Mr Justin: I have tried to do energy minimization in this situation which only existing small molecule in water, I found the structure of organic molecule didn’t become distortions. I think the distortions of organic molecules are due to these

Re: [gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

But what if the coordinates do not match? I mean Glycine may not have the same coordinates after. On Mon, Aug 7, 2017 at 2:48 PM, yujie liu wrote: > > The .top file of protein has included itself all parameters, so now you > only copy gly.gro into protein.gro and changed

[gmx-users] Non Standard residues moving Away

Hi, I am trying to simulate a Protein Ligand system. Now, my system has some non standard residues and I standardized them for AMBER forcefield using ACPYPE. However, when I assemble the gro files of the Proten generated from pdb2gmx and the gro files obtained from ACPYPE, I see that they are not

Re: [gmx-users] Performance values

Indeed, "Wall t" is real application wall-time, nanoseconds/day is the typical molecular dynamics performance unit that corresponds to the effective amount of simulation throughput (note that this however depends on the time-step and without that specified it is not useful to compare to other

[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

Dear Gromacs, I am doing a MD for a protein with glycines. For glycine, I use ) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter and got ) gly.gro ) posre_gly.itp ) topol_gly.top For protein, I use ) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh

Re: [gmx-users] Visualization of xtc file

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi andrea Thank you for replyYes i moved the speed control on the left but it wasnt affected. And now i went to graphical

Re: [gmx-users] Visualization of xtc file

Hi please refer to VMD guide/manual/mailing list. You have different options to "decrease" the motion: 1. in VMD Main there is a speed control, just move to left with mouse or/and 2. in Graphical Representations under Trajectory tab you can increase the number of "Trajectory Smoothing

[gmx-users] Visualization of xtc file

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear gromacs user I am trying to view .gro and .xtc files of my complex by VMD but when i load first .gro and then .xtc files

[gmx-users] 2D maps

Hello all, I have CGMD simulation for a membrane protein embedded in a model membrane with several E. coli lipids, built with /insane/ script. I want to generate colored scaled 2D maps for the membrane thickness and for the lipids distributions for each bilayer leaflet. Could you give some

[gmx-users] amino acid adsorption on metal surface

hello! I am quiet beginner in Gromacs. I want to do adsorption of tryptophan on Au(1 1 1) surface. Please help me that how can I construct the gold surface in gromacs and how to adsorb tryptophan on that surface. Regards --

[gmx-users] converting xtc to pdb without need to tpr file using trjconv

Dear users, Anyone knows how can I use trjconv to convert an xtc file to pdb format without need to tpr file ? Thanks, Neda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] time calculations

Please any one tell me that on what basis the time calculations occurs that is in pico seconds Sent from Mail for Windows 10 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read