Re: [gmx-users] pdb2gmx: how to preserve original ions?

On 7/17/18 9:22 PM, Anderson, Amos wrote: Hi Gromacs users, I’ve never used gromacs before, so sorry if this question has an obvious answer somewhere — it seems like the sort I should have been able to find an answer for… I want to write a python script to prepare an arbitrary pdb for use

[gmx-users] pdb2gmx: how to preserve original ions?

Hi Gromacs users, I’ve never used gromacs before, so sorry if this question has an obvious answer somewhere — it seems like the sort I should have been able to find an answer for… I want to write a python script to prepare an arbitrary pdb for use with gromacs (e.g., does these steps

Re: [gmx-users] problem in energy minimization

http://www.gromacs.org/Documentation/Errors#Stepsize_too_small.2c_or_no_change_in_energy._Converged_to_machine_precision.2c_but_not_to_the_requested_precision On Tue, 17 Jul. 2018, 11:12 pm neelam wafa, wrote: > Hi, > > Dear gromacs users, I am running md simmulation of a protein with a ligand.

Re: [gmx-users] Reaching equilibrium

Monitor your property of interest, then when it has reached a stable value for a length of time (need to consider how long takes to stabilise to how long that should be), then you can start to think it may be at "equilibrium". Depending on the property of interest though, you have to chance if ran

[gmx-users] Fwd: problem in energy minimization

-- Forwarded message -- From: neelam wafa Date: Tue, Jul 17, 2018 at 1:12 PM Subject: problem in energy minimization To: gromacs.org_gmx-users@maillist.sys.kth.se Hi, Dear gromacs users, I am running md simmulation of a protein with a ligand. i have already done it with the

Re: [gmx-users] Incorrect number of parameters in improper dihedral

Hello, In the OPLSAA ffbonded.itp, it is also mentioned that improper torsions for planar groups are implemented in gromacs as proper dihedrals. So, I think you are using the wrong function type here (type 2); you should use type 1 in this case. Hope this helps. Best, Abhishek On Tue, Jul 17,

Re: [gmx-users] resize pre-equilibrated system

Hi Justin, Thank you for getting back to me. After estimating the resulting reduction in system size, in this case I decided to live with the extra water molecules. However, it’s good to know that any system adjusted this way requires both minimization and equilibration. Best, Roman > On Jul

[gmx-users] Reaching equilibrium

Dear all, How to understand whether a system(large system) reaches equilibrium after MD simulation? -- Best regards, *Shyantani Maiti* -- 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] Lennard-Jones mixture with non-standard mixing rules and different interaction cut-offs -- simple way to implement?

Hello all, I'd like to simulate a Lennard-Jones mixture. For simplicity, let's say it's a binary A B mixture. However, sigma_AB and epsilon_AB are set independently (i.e. NOT derived from a standard mixing rule of AA and BB parameters). In addition, I'd like AA, BB, and AB interactions to all

[gmx-users] problem in energy minimization

Hi, Dear gromacs users, I am running md simmulation of a protein with a ligand. i have already done it with the same protein and a different ligand. Now when i run em md run i get following result. Energy minimization has stopped, but the forces have not converged to the requested precision Fmax

Re: [gmx-users] what is the force on the energy group when pullcode is used?

one more question about the pull code. I have outputted the force for pulling the molecule in .xvg file. If I pulled the molecule in Z direction, does the positive sign in front of the force mean the direction of the pulling force is identical to the positive direction of the Z axis? Fan

Re: [gmx-users] Format of xvg file

Hi, Generally there is useful information in the header of the .xvg file, which people might be able to help interpret. They will also want to know what command you ran, and from what version of GROMACS, because these things can vary over time. Mark On Tue, Jul 17, 2018 at 2:37 PM SHYANTANI

Re: [gmx-users] what is the force on the energy group when pullcode is used?

Thanks Justin Fan -- Original -- From: "Justin Lemkul";; Date: Jul 17, 2018 To: "gmx-users"; Subject: Re: [gmx-users] what is the force on the energy group when pullcode is used? On 7/17/18 6:03 AM, 1185201182 wrote: > Dear users > > > I am

[gmx-users] Format of xvg file

Dear all, What should be the format of xvg file for calculating the time correlation function in gromacs? I am using this format(1st and 3rd column are the time steps) 0 -1.73312 0 5.43112 2 -0.84264 2 8.65560 4 -0.89785 4 2.14901 6 1.613256 2.87340 8 -2.32500 8 0.48249 10 1.82224 10

Re: [gmx-users] what is the force on the energy group when pull code is used?

On 7/17/18 6:03 AM, 1185201182 wrote: Dear users I am using the pull code to pull one of molecules in my simulation and the molecule which is pulled is also defined as an energy group in my mdp file, then I output the force in trr file So I wonder if the force on the pulled molecule

Re: [gmx-users] Grompp errors while changing combination rules

On 7/17/18 5:40 AM, Apramita Chand wrote: Dear All, I had enquired earlier about the steps for changing combination rules in GROMOS ff. As I understood from your answers, if I am to take combination rule 3, I can put sigma and epsilon for my atomtypes under the C6 and C12 columns in

Re: [gmx-users] Tilt in the Bilayer

On 7/17/18 3:10 AM, atb files wrote: Dear experts,How can I find the tilt in the lipids of the Bilayer with respect to Bilayer normalAny gromacs tool which can do this.ThanksYogiSent using Zoho Mail gmx bundle and gmx gangle can both do this.

Re: [gmx-users] Problems during installation

Justin, Lovely advice. I'll definitely consider it :) Thank you. Regards, Rajat On Mon, Jul 16, 2018 at 11:15 PM Justin Lemkul wrote: > > > On 7/16/18 1:42 PM, Rajat Desikan wrote: > > Hi Mark, > > > > Thank you for the quick answer. My group is experimenting with a > GPU-heavy > >

[gmx-users] what is the force on the energy group when pull code is used?

Dear users I am using the pull code to pull one of molecules in my simulation and the molecule which is pulled is also defined as an energy group in my mdp file, then I output the force in trr file So I wonder if the force on the pulled molecule in the trr file just includes the force

[gmx-users] Grompp errors while changing combination rules

Dear All, I had enquired earlier about the steps for changing combination rules in GROMOS ff. As I understood from your answers, if I am to take combination rule 3, I can put sigma and epsilon for my atomtypes under the C6 and C12 columns in ffnonbonded.itp and these numbers will be interpreted

[gmx-users] Tilt in the Bilayer

Dear experts,How can I find the tilt in the lipids of the Bilayer with respect to Bilayer normalAny gromacs tool which can do this.ThanksYogiSent using Zoho Mail -- Gromacs Users mailing list * Please

Re: [gmx-users] Pressure Calculation in Gromacs

Hi, That depends what your other inputs are. See the reference manual, chapter 2. Mark On Tue, Jul 17, 2018 at 5:05 AM Brandon Wiebe wrote: > Thank you, Justin. > > So if I wanted to simulate a system of Lennard-Jones particles under the > NPT ensemble using reduced units, would I need to set