[gmx-users] Cutoff

Hi everyone, I want to calculate gangle within a cutoff region. How can I give cutoff for calculating gmx gangle. Thanks -- 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] The difference between selecting residue groups with r (residue) or ri (residue index) under gmx make_ndx

Dear GROMACS staff, Thank you very much for reading this email. I have a question on the selection of residue groups when I use gmx make_ndx: What is the *difference *between selecting residues with *r (residue) or ri (residue index)*? Since the number of atoms after the selection differs

Re: [gmx-users] Building different size membranes using gromacs 5.1.4

Note that the solution Dallas suggested will work (along with changing the resulting box dimensions), but that it may lead to clashes at periodic boundaries. You may need to re-minimize (perhaps with soft-core potentials if there are serious clashes) and re-equilibrate, which would probably defeat

Re: [gmx-users] Building different size membranes using gromacs 5.1.4

Select molecules within the appropriate x y coordinates (if that is the plane that the membrane is in) that will provide that number of molecules, http://manual.gromacs.org/current/onlinehelp/selections.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of

Re: [gmx-users] Printing energies at every step of energy minimization

On 8/8/19 5:04 PM, Wahl, David M wrote: Hello, I am working on parameterizing a small molecule using GROMACS and am having issues during energy minimization. I want the program to output the potential energy at every step, except it only prints at the initial step. The program shows

[gmx-users] Printing energies at every step of energy minimization

Hello, I am working on parameterizing a small molecule using GROMACS and am having issues during energy minimization. I want the program to output the potential energy at every step, except it only prints at the initial step. The program shows that it takes another 7 steps, although it does

Re: [gmx-users] Change forcefield directory

Dear Neena, You can either copy the force field folder to your working folder (I usually go for this) and then it should show up in the interactive window or add the flag -ff and include the path to the folder like so: pdb2gmx -ff /programs/x86_64-linux/gromacs/2018.4/share/gromacs/top/ Good

Re: [gmx-users] Invalid particle type

On 8/9/19 11:09 AM, afsaneh maleki wrote: Dear All I generated topology.top file for Gold surface with g_pdb2gmx - VERSION 4.5.5 using oplsaa force field as the following: ; Command line was: ; g_pdb2gmx -f Au110.gro -p 1 -o 1 ; Force field was read

Re: [gmx-users] Change forcefield directory

On 8/8/19 2:32 PM, Dawid das wrote: Hi, You need to set the GMXLIB to directory with a modified forcefield. Just copy all other files apart from aminoacids.rtp to a new directory with a forcefield. There is no need to change GMXLIB (this can affect other things!) - all one needs to do is

Re: [gmx-users] Change forcefield directory

Hi, You need to set the GMXLIB to directory with a modified forcefield. Just copy all other files apart from aminoacids.rtp to a new directory with a forcefield. Also, if you want to be sure that you use a correct force field, you can modify first line of forcefield.doc file into something like

[gmx-users] Change forcefield directory

Hello gromacs users, I had to add a new residue into forcefield, that required copying aminoacid.rtp file into my home folder (as gromacs is installed on a shared network). During pdb2gmx, how can I redirect the following to my home folder? Where can I edit this change in forcefield directory?

Re: [gmx-users] Relation between tau_t and nstxout

Hi, On Thu, 8 Aug 2019 at 18:41, Neena Susan Eappen < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > I am using Nose-hoover thermostat, is it correct to say that tau_t has to > be less than or equal to nstxout/ nstvout? No. tau_t describes the rigidity of the coupling.

[gmx-users] Building different size membranes using gromacs 5.1.4

I want to extract 128 DPPC bilayer section(1/4) from pre-equilibrdated 512 DPPC bilayer.How can I do this with gromacs 5.1.4? Any assistance you can provide would be greatly appreciated. Thanking you in advance. Regards, dananjana -- Gromacs Users mailing list * Please search the archive at

[gmx-users] (no subject)

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[gmx-users] Relation between tau_t and nstxout

Hello gromacs users, I am using Nose-hoover thermostat, is it correct to say that tau_t has to be less than or equal to nstxout/ nstvout? Because I do not want to record position and velocity before the temperature has been relaxed to target temperature? Please correct me. Thank you, Neena --

[gmx-users] Invalid particle type

Dear All I generated topology.top file for Gold surface with g_pdb2gmx - VERSION 4.5.5 using oplsaa force field as the following: ; Command line was: ; g_pdb2gmx -f Au110.gro -p 1 -o 1 ; Force field was read from the standard Gromacs share directory. ;

Re: [gmx-users] Gromacs 4.5.7 compatibility with Titan X GPU

Hi, Unfortunately that version of GROMACS hasn't been tested or supported in well over five years, so probably it is simply incompatible with modern GPUs. You could try explicit solvent in modern GROMACS, which might be comparably fast with that old version :-) Or AMBER if you really need

Re: [gmx-users] Gromacs 4.5.7 compatibility with Titan X GPU

Any feedback would be appreciated. Thank you. On Fri, Aug 2, 2019 at 11:29 AM Timothy Hurlburt wrote: > Hi, > I am trying to install GPU accelerated Gromacs 4.5.7 for use with implicit > solvent. > I am using an Nividia GM200 [GeForce GTX TITAN X] GPU. > > When I tried to install Gromacs with