[gmx-users] Vmd error

I extended my simulation of a free protein from 100ns to 150ns. Corresponding files are extend.gro and extend.xtc. I applied pbc conditions and my new xtc s newmd.xtc. I tried to visualise my trajectory in vmd I uploaded the extend.gro file and loaded newmd.xtc in gro file. But I couldn't

Re: [gmx-users] Space between the columns in the topology file of Gromacs

Thank you, Best, *Lan Hoa* 2017-06-15 17:02 GMT-05:00 Mark Abraham : > Hi, > > Those are simply fields separated by whitespace. Columns not relevant. > > Mark > > On Thu, 15 Jun 2017 22:10 lan hoa Trinh wrote: > > > Dear Gromacs society, > > I

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

kindly tell me sir how i can i add residue On Thu, Jun 15, 2017 at 2:04 AM, Rana Rehan Khalid wrote: > thanks justin > actually i want to know that how these values of column (atom name, type, > charge and charge group) we obtain for oxygen bonded with heme fe. is there >

Re: [gmx-users] Problems with IMD in Gromacs 2016.3

Hi, Those are freely available to register, though I don't have a link to hand. Mark On Fri, 16 Jun 2017 00:58 Charles Laughton < charles.laugh...@nottingham.ac.uk> wrote: > Hi Mark, > > Redmine.gromacs.org asks me for a username and password – I have neither. > > Regards, > > Charlie > > > On

Re: [gmx-users] Space between the columns in the topology file of Gromacs

Hi, Those are simply fields separated by whitespace. Columns not relevant. Mark On Thu, 15 Jun 2017 22:10 lan hoa Trinh wrote: > Dear Gromacs society, > I wonder if there is the default for the space between the columns in the > topology file, for example: > [ bonds ] >

Re: [gmx-users] Problems with IMD in Gromacs 2016.3

Hi Mark, Redmine.gromacs.org asks me for a username and password – I have neither. Regards, Charlie On 15/06/2017, 19:10, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham"

[gmx-users] Space between the columns in the topology file of Gromacs

Dear Gromacs society, I wonder if there is the default for the space between the columns in the topology file, for example: [ bonds ] ;ai aj funcr0(nm) Kb 12 1 3.805916447e-01 2.0e+04 23 1 3.788218579e-01 2.0e+04 3

Re: [gmx-users] Errors during pull constrained NPT simulation for permeability calculations.

Dear Yogesh: you either need to make the system larger in the dimension(s) of your pulling or you need to not pull out to such a far distance. Once you straighten that out, and if the lincs problems remain, then we can tackle that separately. What are your mdp options for pulling? Maybe you

Re: [gmx-users] Problems with IMD in Gromacs 2016.3

Hi, Redmine.gromacs.org is the place. Please add enough inputs to reproduce the problem! Mark On Thu, 15 Jun 2017 20:42 Charles Laughton < charles.laugh...@nottingham.ac.uk> wrote: > Hi Carsten, > > Can you explain how I file a bug report? Do I need to be subscribed to the > gmx-developers

Re: [gmx-users] Problems with IMD in Gromacs 2016.3

Hi Carsten, Can you explain how I file a bug report? Do I need to be subscribed to the gmx-developers list or something? Regards, Charlie On 15/06/2017, 13:50, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Kutzner, Carsten"

[gmx-users] Error when performing MD with heavy atoms frozen

Hi there, I am new to GROMACS, went through Lysozeme in Water tutorial and everything runs smoothly. I then tried to immobilize all heavy atoms (except H) in md.mdp file by specifying freezegrps = Protein-H ; Freeze all heavy atoms freezedim= Y Y Y ;

Re: [gmx-users] precision of input gro file

Hi Mark, Great! Thanks a lot. I try with the g96 format. Best, -Yu 2017-06-15 15:04 GMT+01:00 Mark Abraham : > Hi, > > Yes g96 is a good format for that > > Mark > > On Thu, 15 Jun 2017 14:38 Yu Ogawa wrote: > > > Hi Mark, > > Thanks for suggestions.

Re: [gmx-users] -bash: ngmx: command not found

Hi, You need also the development library part for your x system, so it can be compiled against. Often in a different but related download. Mark On Thu, 15 Jun 2017 16:14 Karchevskaya, Anastasia < anastasia.karchevskaya...@ucl.ac.uk> wrote: > Dear Gromacs Users, > > I can’t run ngmx. > >

[gmx-users] -bash: ngmx: command not found

Dear Gromacs Users, I can’t run ngmx. Gromacs version 4-6-7; tried to re-install already. Machine: Mac (OS Sierra) X11/XQuartz: XQuartz 2.7.11 (xorg-server 1.18.4) Lesstif: lesstif 0.95.2 Installed with brew What else should I do to make it work? What am I doing wrong? Thank you Ana --

Re: [gmx-users] precision of input gro file

Hi, Yes g96 is a good format for that Mark On Thu, 15 Jun 2017 14:38 Yu Ogawa wrote: > Hi Mark, > Thanks for suggestions. I will take a look at the g96 format. > I try to deform a part of polymer crystal with a small displacement, and > then relax the structure in MD while

[gmx-users] Errors during pull constrained NPT simulation for permeability calculations.

Hi Experts, I am doing simulation for permeability calculation. In my simulation, water molecule is constrained (inside the Bilayer) at fixed distance from centre of the Bilayer. And another constrained in bulk water. I am doing equilibration with V-rescale(thermostat) and berendsen(for

Re: [gmx-users] Problems with IMD in Gromacs 2016.3

Hi Charlie, I just made a quick check with 5.1 and 2016 and I also see the problem that you described. For me IMD works with 5.1, but not with 2016, but I don't know why. Could you file a bug report? Thank you, Carsten > On 14. Jun 2017, at 18:05, Charles Laughton >

[gmx-users] General questions about topology building

So the following question, if I want to change a few residues in a system that is already made (equilibrated, a protein in a lipid membrane), how should i go about that? What would be the protocol? I did it this way -> i first made a pdb out of the last frame (changed the 3 residues in

Re: [gmx-users] precision of input gro file

Hi Mark, Thanks for suggestions. I will take a look at the g96 format. I try to deform a part of polymer crystal with a small displacement, and then relax the structure in MD while keeping the displacement by constraint. As the displacement can be very small, I want to have an input structure file

Re: [gmx-users] precision of input gro file

Hi, Usually one doesn't need a higher precision text file. The g96 format does work for this, but you should probably be using a real trajectory or checkpoint format for whatever you are trying to do. That would have been good to describe, rather than assuming the form of the solution ;-) Mark

Re: [gmx-users] In vacuo MD

Hi, Check again the mdp options. Zero may not be the right choice for all of them Mark On Thu, 15 Jun 2017 13:56 Linus Johannissen < linus.johannis...@manchester.ac.uk> wrote: > Thanks Justin, > > I'm using Gromacs 4.6.1. I don't think changing energygrps is going to > change anything as I

Re: [gmx-users] In vacuo MD

Thanks Justin, I'm using Gromacs 4.6.1. I don't think changing energygrps is going to change anything as I have the same problem in the energy minimisation (zero LJ (SR) and Coulomb (SR) energies). However, I found that if the simulation seems to run fine if I use a cutoff of 999 instead of 0.

Re: [gmx-users] precision of input gro file

Hi Eric, Thanks for replying. I may be wrong, but what I understand from the online manual is that we have a higher precision in MD calculation (as in trr file). I am not sure if grompp recognizes a higher precision than 3 decimal places. When I did editconf with a gro file with higher precision

Re: [gmx-users] precision of input gro file

Hello Yu, Read this carefully. http://manual.gromacs.org/online/gro.html As far as I know, Gromacs will accept gro files with high precision if the input file follows this format. Best, Eric > On Jun 15, 2017, at 4:33 AM, Yu Ogawa wrote: > > Hello gmx users, > Can we

[gmx-users] precision of input gro file

Hello gmx users, Can we increase a precision of input structure file more than 3 decimal places? Thank you for your help! Yu -- 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

Re: [gmx-users] How to read .dat file

The file rms.xvg contains only RMSD values against the reference PDB structure; what I need to know is the contents of RMSD matrix between 2 trajectories. Qing At 2017-06-15 15:17:08, "Dd H" wrote: >I think this link should be helpful.

[gmx-users] pdb2gmx peptide nanotube

*Dear Gromacs users,* I am trying to simulate a peptide nanutube composed by 8 cyclics.When I execute pdb2gmx with the options -missing and -ter (selecting manually None), as I have seen in the Gromacs list, I get this error: pdb2gmx -f tube.pdb -ter -missing -ignh8 out of 8 lines of

[gmx-users] Errors during pull constrained NPT simulation for permeability calculations.

Hi Experts, I am doing simulation for permeability calculation. In my simulation, water molecule is constrained (inside the Bilayer) at fixed distance from centre of the Bilayer. And another constrained in bulk water. I am doing equilibration with V-rescale(thermostat) and berendsen(for

[gmx-users] DIHEDRAL SCAN

Hi, How to run potential energy surface scan for a molecule using gromacs?. What are the steps? Thanks, Neha -- 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

Re: [gmx-users] How to read .dat file

I think this link should be helpful. http://manual.gromacs.org/programs/gmx-rms.html You can have a look at rms.xvg file, it contains rmsd values. Best regards, Dading Huang On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv wrote: > I generated a .dat file with the following

Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

thanks justin actually i want to know that how these values of column (atom name, type, charge and charge group) we obtain for oxygen bonded with heme fe. is there any program through which i find the parameter file for oxygen with heme and nitric oxide with heme iron. if i just add the atom name