Re: [gmx-users] 500ns simulation

Increase the number of steps On Wed, 4 Jul 2018, 12:07 pm Quyen V. Vu, wrote: > Take simulation time= timestep (dt) * number of steps (nstep) > > On Wed, Jul 4, 2018, 12:48 Soham Sarkar wrote: > > > Change in the number of time steps > > > > On Wed, 4 Jul 2018, 10:54 am Raag Saluja, wrote: > >

Re: [gmx-users] 500ns simulation

Take simulation time= timestep (dt) * number of steps (nstep) On Wed, Jul 4, 2018, 12:48 Soham Sarkar wrote: > Change in the number of time steps > > On Wed, 4 Jul 2018, 10:54 am Raag Saluja, wrote: > > > Hi! > > > > What changes do I make to the mdp files provided by you in the lysozyme > > tu

[gmx-users] Generating N2 topology

Hi All, I'm currently trying to generate the topology for molecular Nitrogen (N2) and am running into some trouble. For reference, the pdb file I have for N2 is as follows: HETATM1 N6B HDZ 0 0.000 0.000 0.553 1.00 0.00 N HETATM2 N6A HDZ 0 0.000

Re: [gmx-users] 500ns simulation

Change in the number of time steps On Wed, 4 Jul 2018, 10:54 am Raag Saluja, wrote: > Hi! > > What changes do I make to the mdp files provided by you in the lysozyme > tutorial, to make it a 500ns simulation? > > Thanks in advance! > > Regards, > Raag > -- > Gromacs Users mailing list > > * Plea

[gmx-users] 500ns simulation

Hi! What changes do I make to the mdp files provided by you in the lysozyme tutorial, to make it a 500ns simulation? Thanks in advance! Regards, Raag -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

Re: [gmx-users] [gmx-developers] Quick test after installation

The developers' list is for discussion of code and other development issues. Please post normal user questions like this on the gmx-users mailing list. You'll find the answer to your question here: http://manual.gromacs.org/documentation/current/install-guide/index.html#testing-gromacs-for-c

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

On 7/3/18 6:52 PM, Eric Smoll wrote: Justin, Thanks again for the response and the guidance. Your 2015 JCC paper on the subject was very helpful. Your code uses a different thole_polarization format. Currently, Gromacs uses the following format [ thole_polarization ] ; i j k l fun

Re: [gmx-users] Shell (Drude) model for polarization in GROMACS

Justin, Thanks again for the response and the guidance. Your 2015 JCC paper on the subject was very helpful. Your code uses a different thole_polarization format. Currently, Gromacs uses the following format [ thole_polarization ] ; i j k l function-number thole-a-parameter alpha_i

[gmx-users] Rerun

Dear users, Will the .trr files produced from rerun of .xtc files be the same if it was produced during the original MD simulation? Kind regards,Ahmed -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can'

Re: [gmx-users] genion problem with topology

On 7/3/18 1:47 PM, gangotri dey wrote: Dear all, I have replaced one water molecule in the solvent with a Cl atom using genion. My syntax is as follows: gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1 -nname CL I have generated the ions.tpr using the ion.mdp file as i

Re: [gmx-users] genion problem with topology

What forcefield are you using? Check if CL is defined in your forcefield (it's probably not, which is why you are getting the error). Each type under [ molecules ] must have a corresponding [ moleculetype ] section defined somewhere in your forcefield files. On 3 July 2018 at 18:47, gangotri dey

[gmx-users] genion problem with topology

Dear all, I have replaced one water molecule in the solvent with a Cl atom using genion. My syntax is as follows: gmx_mpi genion -s ions.tpr -o solvate.gro -p topol.top -pname NA -nn 1 -nname CL I have generated the ions.tpr using the ion.mdp file as in the tutorial from Bevan group. I see that

Re: [gmx-users] Pulled group moves randomly while doing umbrella sampling

That error is solved by switching to *pull_coord1_geometry = direction-periodic* to let it move over periodic boundary conditions as described here: http://manual.gromacs.org/online/mdp_opt.html#pull On Sat, Jun 30, 2018 at 12:07 AM Chenlin Lu wrote: > Hello, > > > I am doing umbrella sampling

Re: [gmx-users] AdResS feature in gromacs

Hello Eduardo, I forgot that water of course does not require 1-4 interactions, so that's while the tf generation worked (VOTCA would not have generated a tablep.xvg file if it had been required but already caused problems there) and the simulation with protein didn't. Again, copying the tabl

[gmx-users] AdResS feature in gromacs

Hello Jan Thank you for your reply Exactly, VOTCA generated the thermoforce so it was able to perform an Adress simulation. I've looked more carefully at the files generated by VOTCA and could not find a file that might be this tablep.xvg. But I think that this problem is related to the fact th

Re: [gmx-users] benchmarks

On 7/3/18 11:53 AM, Mahmood wrote: You don't need a PDB file for anything if you have conf.gro. With topol.tpr, you also don't need to regenerate any .tpr file, unless you're trying to compare with a different version, but you can generate a topology from conf.gro and use the provided .mdp file

Re: [gmx-users] benchmarks

>You don't need a PDB file for anything if you have conf.gro. With >topol.tpr, you also don't need to regenerate any .tpr file, unless >you're trying to compare with a different version, but you can generate >a topology from conf.gro and use the provided .mdp file to create a new >.tpr >file.

Re: [gmx-users] adkgromacstutorial error

Thanks for reporting the errors with the tutorial and possible fixes. On Jul 3, 2018, at 5:37 AM, Justin Lemkul wrote: > On 7/3/18 8:32 AM, Mahmood wrote: >> The tutorial contents look a bit outdated > Well the main page says that the release date is Jul 3 and it is compatible > with 2018. I a

Re: [gmx-users] AdResS feature in gromacs

Hello Eduardo, tablep.xvg contains the tabulated potential for 1-4 interactions, which are non-bonded interactions inside a molecule that usually only differ by the Lennard-Jones parameters sigma/epsilon (or C6/C12) but not the general shape of the potential. Since these should only occur in t

[gmx-users] AdResS feature in gromacs

Hi, I forgot to mention my gromacs version. I'm using gromacs 5.1.5. I don't know since what version adress was deprecated. I just assumed that this version would work cause the Adress feature is presented in its manual. Thanks Eduardo ___

Re: [gmx-users] AdResS feature in gromacs

Hi, Which version of GROMACS are you using? I do recall a bug related to this input file, which did get fixed, but I don't recall whether we fixed it before AdRessS was removed from GROMACS. Mark On Tue, Jul 3, 2018 at 2:24 PM Eduardo Diniz wrote: > Hello everyone, > > > I'm trying to run an s

[gmx-users] freezing or constraining

Dear all, In studying the solid surfaces, I have noticed that some people freeze or constrain the slab's atoms to their initial or relaxed coordinates, I was wondering if doing that is a proper approach? If it is, where the penalty energy of being frozen or constrained goes? I can understand that

Re: [gmx-users] benchmarks

On 7/3/18 9:13 AM, Mahmood wrote: Hi,The benchmark package [1] has no readme on how to run the benchmarks. In each folder I see conf.gro, *.mdp and topol.tpr. Following the tutorials, there is no pdb file there. I need that to build tpr file and that is used in gmx mdrun. Can someone shed a

[gmx-users] AdResS feature in gromacs

Hello everyone, I'm trying to run an simulation in gromacs with AdResS, where water is treated as fine grained in the region close to the protein and as coarse-grained in the farthest layers. I've already generated the tabulated potential for coarse-grained water with the VOTCA package and als

[gmx-users] benchmarks

Hi,The benchmark package [1] has no readme on how to run the benchmarks. In each folder I see conf.gro, *.mdp and topol.tpr. Following the tutorials, there is no pdb file there. I need that to build tpr file and that is used in gmx mdrun. Can someone shed a light on that? Where could I find more

Re: [gmx-users] adkgromacstutorial error

On 7/3/18 8:32 AM, Mahmood wrote: The tutorial contents look a bit outdated Well the main page says that the release date is Jul 3 and it is compatible with 2018.I changed tau-p to just one value (tau-p = 2.5) Well, the home page says the tutorials "should be compatible" with the listed ve

Re: [gmx-users] adkgromacstutorial error

>The tutorial contents look a bit outdated Well the main page says that the release date is Jul 3 and it is compatible with 2018.I changed tau-p to just one value (tau-p = 2.5) Now, I get Program: gmx grompp, version 2018 Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2682) Fatal err

Re: [gmx-users] adkgromacstutorial error

On 7/3/18 7:48 AM, Mahmood wrote: Hi,Following adkgromacstutorial, at the energy minimization step [1], I hit an error. All previous steps are fine. Command line:   gmx grompp -f md.mdp -p ../top/4ake.top -c ../posres/posres.pdb -o md.tpr -maxwarn 3 Yikes! -maxwarn 3? Very dangerous...

[gmx-users] adkgromacstutorial error

Hi,Following adkgromacstutorial, at the energy minimization step [1], I hit an error. All previous steps are fine. Command line:   gmx grompp -f md.mdp -p ../top/4ake.top -c ../posres/posres.pdb -o md.tpr -maxwarn 3 ERROR 1 [file md.mdp, line 94]:   Right hand side '2.5 2.5' for parameter

Re: [gmx-users] Updated tutorials and new website

Hi Justin, that sounds like a great plan. Thanks for initiating something like this. Iris, I am up for helping with some of the tutorials, especially, the ED simulations if you need any help. That is something I have some experience with as well. Shreyas On Tue, Jul 3, 2018 at 1:13 PM Justin

Re: [gmx-users] Updated tutorials and new website

The enthusiasm for writing new tutorials is very encouraging, and admittedly has taken me a bit by surprise. Let me "pull back the curtain" on what I am thinking regarding my own site and how others might engage. I am about to submit an article detailing my tutorials and the theoretical und