[gmx-users] (no subject)

Hello all How to handle HS14 generated by ATB server in topology file? Regards -- 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 http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] How to perform final MD simulation after extending a NPT simulation

Dear all, *I used following command to extend a NPT simulation* 1) gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr gmx mdrun -deffnm tpxout -cpi npt.cpt -v but the analysis " gmx energy -f *tpxout*.edr -o pressure.xvg " shows only the extended part; How to append the extend

Re: [gmx-users] Protein-ligand binding Cut-offs

Yes, remove figure reference, use figures from us, and insert reference at the same place for the Software: "Figure made with MacMolPlt" http://www.sciencedirect.com/science/article/pii/S109332639929 Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [

Re: [gmx-users] Protein-ligand binding Cut-offs

Hi, No, that's not a prerequisite, but it is one approach. Mark On Tue, Jun 20, 2017 at 8:16 PM Pandya, Akash wrote: > Hi, > > Is the pre-requisite for this command a separate index file for the > glycine molecules I have? > > Akash > > -Original Message- >

Re: [gmx-users] Protein-ligand binding Cut-offs

Hi, Is the pre-requisite for this command a separate index file for the glycine molecules I have? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 16 June 2017

Re: [gmx-users] a problem about ewald geometry=3dc

Dear Philip Thanks for your helpful advice Actually, my simulation case is a slab of water that is covered by monolayer in just one surface and the other surface is free and sometimes some of water molecules (small number) escape from it. So is 3dc option still applicable or I should return to

Re: [gmx-users] Error running GMX 5.14

Hi, # make initial gro and .top somehow gmx grompp -f whatever -c initial -p initial -o for-genion cp initial.top with-ions.top gmx genion -f for-genion -p with-ions.top -o with-ions gmx grompp -f em -p with-ions -c with-ions -o ready-for-em gmx mdrun -s ready-for-em Mark On Tue, Jun 20, 2017

Re: [gmx-users] (no subject)

Thanks sir for your support. Dear justin sir do u hv any more ideas On 20 Jun 2017 18:54, "Mark Abraham" wrote: > Hi, > > Follow ATB's directions for how to use the files it produces. If ATB is > creating a new atom type, then it will be supplying parameters that

Re: [gmx-users] Error running GMX 5.14

Precisely. Thanks. Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [

Re: [gmx-users] Error running GMX 5.14

On 6/20/17 10:36 AM, Sergio Manzetti wrote: One simple question, where does one get the sytem input for genion, as it only want tpr, unless one uses grompp? Yes, you have to use grompp on the solvated system to get a .tpr of the system that contains no ions. You pass that .tpr to genion

Re: [gmx-users] Error running GMX 5.14

One simple question, where does one get the sytem input for genion, as it only want tpr, unless one uses grompp? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr.

Re: [gmx-users] Error running GMX 5.14

On 6/20/17 10:32 AM, Sergio Manzetti wrote: Let me see if I have it right. After doing the minimization of the system without ions, I add ions to the minimized system and replace the waters. I see no point in doing multiple rounds of minimization like this. Just build the whole system

Re: [gmx-users] Error running GMX 5.14

Let me see if I have it right. After doing the minimization of the system without ions, I add ions to the minimized system and replace the waters. Then I use grompp to set up the sim with the output tpr from the genion command as -c file, and the original topology ? Sergio Sergio

Re: [gmx-users] Error running GMX 5.14

OK Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 

Re: [gmx-users] Error running GMX 5.14

On 6/20/17 10:21 AM, Sergio Manzetti wrote: Thanks Justin. So it is right to run the simulation without ions, then add ions, then re-run with ions with the new topolgy? I wouldn't run a simulation without ions, no. Please consult a basic tutorial about the conventional steps for doing a

Re: [gmx-users] Error running GMX 5.14

Thanks Justin. So it is right to run the simulation without ions, then add ions, then re-run with ions with the new topolgy? Sergio Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894

Re: [gmx-users] Error running GMX 5.14

On 6/20/17 10:14 AM, Sergio Manzetti wrote: I run the simulations on the solvated DNA without adding ions. Then at the end, I added ions to the output tpr of the simulation. At this stage I waanted then to run the simulaiton with the new tpr. But that does not work. How did you add ions

Re: [gmx-users] a problem about ewald geometry=3dc

Dear Ali, to use the 2D correction you only have to make sure that your box height is at least 3 times larger than your slab. This does not depend on the explicit position of your slab. So pbc=xyz does not make any problems, if your atoms always “stay” in a thin slab and do not move around in

Re: [gmx-users] Error running GMX 5.14

I run the simulations on the solvated DNA without adding ions. Then at the end, I added ions to the output tpr of the simulation. At this stage I waanted then to run the simulaiton with the new tpr. But that does not work. Is there a tutorial online on how to add Na to DNA with command line?

Re: [gmx-users] (no subject)

Hi, Follow ATB's directions for how to use the files it produces. If ATB is creating a new atom type, then it will be supplying parameters that belong in the [atomtypes] directive, and their site needs to give you instructions for how to get those recognized. Search their website and ask on their

Re: [gmx-users] (no subject)

Thanks for your suggestion. One more thing In topology file generated by ATB, there is HS14 atomtype and i am getting error FATAL error ATomtype HS14 not found How to handle this error? Kindly suggest On Tue, Jun 20, 2017 at 12:18 PM, Mark Abraham wrote: > Hi, > >

Re: [gmx-users] Error running GMX 5.14

Hi, On Tue, Jun 20, 2017 at 2:41 PM Sergio Manzetti < sergio.manze...@fjordforsk.no> wrote: > I can add ions to the final system, after having simulated it without > ions. But what would the point be? > This is the strange thing, genion treats only tpr files, and not gro files > with solvated

Re: [gmx-users] Error running GMX 5.14

On 6/20/17 8:27 AM, Sergio Manzetti wrote: I can add ions to the final system, after having simulated it without ions. But what would the point be? This is the strange thing, genion treats only tpr files, and not gro files with solvated states The .tpr file fed to genion is that of a

Re: [gmx-users] Difference between Err. Est. And RMSD

On 6/20/17 7:44 AM, jay patil wrote: Hi all, When we get averages from energy file using gmx energy -f *.edr Output shows Average Err.Est RMSD Tot-Drift. Which one among Err.Est or RMSD should I use to show error bars in the plot. By definition I know RMSD, what is formula for Err.Est. See

[gmx-users] Fwd: a problem about ewald geometry=3dc

Hello to all Dear Gromacs Users I'm modeling a lipid monolayer with vacuum space on top of it and with periodic boundary conditions in xyz directions. the vacuum space is about 10nm to minimize any possible effect of periodicity. for using ewald summation as manual mentions : *"The geometry to

Re: [gmx-users] Error running GMX 5.14

I can add ions to the final system, after having simulated it without ions. But what would the point be? This is the strange thing, genion treats only tpr files, and not gro files with solvated states Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ |

Re: [gmx-users] Error running GMX 5.14

On 6/20/17 8:22 AM, Sergio Manzetti wrote: Maybe someone can suggest a method to add ions to the system without that they appear as water molecules? The job of genion is to replace water molecules with ions. There is no way that grompp can turn one into the other; you would get a fatal

Re: [gmx-users] Error running GMX 5.14

Maybe someone can suggest a method to add ions to the system without that they appear as water molecules? The em looks like this: define = integrator = steep emtol = 100.0 emstep = 0.0001 nsteps = 1 ; output frequency nstxout = 50 nstvout = 0 nstfout = 0 nstlog = 50 nstenergy =

Re: [gmx-users] Error running GMX 5.14

Maybe someone can suggest a method to add ions to the system without that they appear as water molecules? The em looks like this: define = integrator = steep emtol = 100.0 emstep = 0.0001 nsteps = 1 ; output frequency nstxout = 50 nstvout = 0 nstfout = 0 nstlog = 50 nstenergy =

Re: [gmx-users] Error running mdrun em with Sodium ions in GMX 5.14

On 6/20/17 8:04 AM, Sergio Manzetti wrote: Hi, I have a system with DNA and water, and given the charge of the DNA of -20, genion was used to add +20 charge to the gro file. The energy minimization step gives then a warning: WARNING 2 [file em.mdp]: The sum of the two largest charge group

Re: [gmx-users] Error running GMX 5.14

What does your *.mdp file look like? Its hard to judge what the next step should be from what you've given so far. -Micholas === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

[gmx-users] Error running mdrun em with Sodium ions in GMX 5.14

Hi, I have a system with DNA and water, and given the charge of the DNA of -20, genion was used to add +20 charge to the gro file. The energy minimization step gives then a warning: WARNING 2 [file em.mdp]: The sum of the two largest charge group radii (16.704304) is larger than rlist

Re: [gmx-users] Topology generation of molecules

Channa, What are you trying to use the Topology for? MD or Analysis of a trajectory from some other piece of software? Justin is right, if you want to run MD than you can't just use one force-field server to generate another, as each one has will give output for different force-fields and each

[gmx-users] Error running GMX 5.14

Hi, I have a system with DNA and water, and given the charge of the DNA of -20, genion was used to add +20 charge to the gro file. The energy minimization step gives then a warning: WARNING 2 [file em.mdp]: The sum of the two largest charge group radii (16.704304) is larger than rlist

Re: [gmx-users] Difference between Err. Est. And RMSD

​Hi, It is stated in the program's description (gmx energy -h): "An error estimate of the average is given based on a block averages over 5 blocks using the full-precision averages. The error estimate can be performed over multiple block lengths with the options -nbmin and -nbmax. Note that in

Re: [gmx-users] Re : Unable to generate umbrella histogram and PMF curve

On 6/19/17 10:57 PM, Norfarisha Mohd Fadil wrote: Dear Justin, I have checked the log file for the particular xvg file and found that there's no simulation (?) being ran as compared to the other log files that generated the force profile for their respective xvg files. The info I have

Re: [gmx-users] Topology generation of molecules

On 6/20/17 12:21 AM, Abid Channa wrote: If PRODRG is not giving suitable results . Can I use Antechamber output in GROMACS for the topology generation of molecules ? . PRODRG is for GROMOS, Antechamber is for AMBER. You can't simply replace one with the other because the force fields are

Re: [gmx-users] Adding multiple different ligands with acpype

On 6/20/17 5:54 AM, Vytautas Rakeviius wrote: Hello, I try to add multiple and different ligands with acpype and bump into issue "Invalid order for directive atomtypes" discussed before (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2008-July/035223.html)I can comment out

[gmx-users] Difference between Err. Est. And RMSD

Hi all, When we get averages from energy file using gmx energy -f *.edr Output shows Average Err.Est RMSD Tot-Drift. Which one among Err.Est or RMSD should I use to show error bars in the plot. By definition I know RMSD, what is formula for Err.Est. Please help. Thanks Yogesh -- Gromacs Users

Re: [gmx-users] how to get omega angles for a trajectory?

Hi, The legends are earlier in the file. See also gmx help chi, perhaps Mark On Tue, 20 Jun 2017 13:38 Seera Suryanarayana wrote: > Dear gromacs users, > I would like to compute omega angles for a trajectory which I have > simulated. when I use "gmx chi" command I got

[gmx-users] how to get omega angles for a trajectory?

Dear gromacs users, I would like to compute omega angles for a trajectory which I have simulated. when I use "gmx chi" command I got some 5 column data with S1 S2 para meters. I didn't understand that data. Kindly tell me how do I get omega angles for trajectory? Thanks in advance Surya Graduate

[gmx-users] Adding multiple different ligands with acpype

Hello, I try to add multiple and different ligands with acpype and bump into issue "Invalid order for directive atomtypes" discussed before (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2008-July/035223.html)I can comment out other ligands leaving one and then it seems OK. I do

Re: [gmx-users] Pull in a channel

Is PLUMED/Gromacs a good solution to do it ? Cheers, FR 2017-06-19 13:04 GMT+02:00 François-Régis Chalaoux : > Hi All, > > I would like to pull a ligand in a channel from my protein and calculate > the PMF with Umbrella sampling. > > How to define in the md_pull.mdp

Re: [gmx-users] (no subject)

Hi, You don't need a file in the gro format. You need coordinates that match the topology present in any supported file format, eg pdb or g96 etc. Mark On Tue, 20 Jun 2017 09:01 Shivangi Agarwal wrote: > Hello > > I used the ATB server for generation of topology

[gmx-users] (no subject)

Hello I used the ATB server for generation of topology file following Gromacs Turorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html