[gmx-users] Error in ions.tpr generation

Dear gmx experts, The ligand molecule was refined and optimized using G03 calculation and .itp was generated using the ATB server. Still, I am getting the following error, dirctly copied from the terminal. And I am unable to generate any extension files in GROMACS using this .itp. $ gmx grompp

[gmx-users] regarding calculation on shear viscosity

-- Forwarded message - From: Madhurima Jana Date: Thu, Feb 27, 2020 at 12:10 PM Subject: Re: problem regarding calculation on shear_viscosity To: shakuntala dhurua Dear All, I have calculated shear viscosity (from 5 ns production trajectory) of bulk > water (900 water

[gmx-users] Proximal RDF of water around protein?

Hi all, Is it possible to calculate proximal RDF of water around protein using gromacs? If not what other programs can I use? Please suggest me. Thanks, Rajeswari -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] regressiontests/complex (Failed)

-How to solve this problem while installing GROMACS-2018.8 on Dell Tesla C2050. -Previously I installed GROMACS-2018.4 had same problem (one test regressiontests/complex failed) still installed. How does this effect simulation? What kind of error we get if we use gromacs even after failing this

Re: [gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy"

On 2/26/20 8:10 PM, Anh Mai wrote: Hi all, Could someone please help me? I have a question about the *temperature outputs *from the two packages "gmx traj" and "gmx energy." I used the two packages to export the Temperature of a "Protein" group. Here is what I did. 1. gmx traj -f

[gmx-users] Fwd: Temperature Output - different b/w "gmx traj" vs. "gmx energy"

Hi all, Could someone please help me? I have a question about the *temperature outputs *from the two packages "gmx traj" and "gmx energy." I used the two packages to export the Temperature of a "Protein" group. Here is what I did. 1. gmx traj -f trajectory_with_velocity.trr -s topology.tpr

Re: [gmx-users] Umbrella sampling of peptide-membrane system

Dear John, Thank you very much for your advice. Best regards, Mijiddorj Hi, > > Justin's tutorial is not a fully generalized procedure for umbrella > sampling; it shows a workflow for one specific example which is not always > applicable to other systems. > > In general, you don't have to use

[gmx-users] Can GROMACS compute heat flux?

Hi, I am interested in testing thermal conductivity at the nano-scale. LAMMPS has a command to control thermal flux: https://lammps.sandia.gov/doc/fix_heat.html But, I cannot find an equivalent command in GROMACS. I know that thermostats can be set in GROMACS, but they do not seem to have a

Re: [gmx-users] Fwd: error during ions.tpr genereation.

On 2/26/20 1:26 PM, Neha Tiwari wrote: Dear all, I want to know if there is any error in the .itp file of ligand attached The mailing list does not accept attachments. here, the ligand molecule was refined and optimized using G03 calculation and .itp was generated using the ATB server. As

[gmx-users] Fwd: error during ions.tpr genereation.

Dear all, I want to know if there is any error in the .itp file of ligand attached here, the ligand molecule was refined and optimized using G03 calculation and .itp was generated using the ATB server. As I am unable to generate any extension files in GROMACS using this. Please help. Neha. --

Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

Hi, Can you please check the performance when running on a single GPU 2019 vs 2020 with your inputs? Also note that you are using some peculiar settings that will have an adverse effect on performance (like manually set rlist disallowing the dual pair-list setup, and nstcalcenergy=1). Cheers,

Re: [gmx-users] Fw: cudaFuncGetAttributes failed: out of memory

Hi, Indeed, there is an issue with the GPU detection code's consistency checks that trip and abort the run if any of the detected GPUs behaves in unexpected ways (e.g. runs out of memory during checks). This should be fixed in an upcoming release, but until then as you have observed, you can

Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

Hello, here is a link to the logfiles. https://faubox.rrze.uni-erlangen.de/getlink/fiX8wP1LwSBkHRoykw6ksjqY/benchmarks_2019-2020 If necessary, I can also provide some more log or tpr/gro/... files. Cheers, Andreas On 26.02.20 16:09, Paul bauer wrote: Hello, you can't add attachments to the

Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

Hello, you can't add attachments to the list, please upload the files somewhere to share them. This might be quite important to us, because the performance regression is not expected by us. Cheers Paul On 26/02/2020 15:54, Andreas Baer wrote: Hello, from a set of benchmark tests with

[gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

Hello, from a set of benchmark tests with large systems using Gromacs versions 2019.5 and 2020, I obtained some unexpected results: With the same set of parameters and the 2020 version, I obtain a performance that is about 2/3 of the 2019.5 version. Interestingly, according to nvidia-smi, the

Re: [gmx-users] Normal mode analysis

Where did you obtain your PDB? Is this a known crystal structure or other experimentally derived structure or is it a homology model? Sometimes the initial structures have minor artifacts that make energy minimization difficult. Perhaps a short-restrained MD simulation (10ps perhaps) with

Re: [gmx-users] Normal mode analysis

My structure does not contain any ions. Here are the commands that I used: gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water tip3p -ignh gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5 gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr

Re: [gmx-users] Normal mode analysis

Hmmm How did you prepare the structure? Also, attachments are stripped from emails to the mailing list, can you please provide your mdp file as plain text in your reply. === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge

Re: [gmx-users] Normal mode analysis

Is your build of GROMACS using double precision? NMA typically is performed with double precision, which is not the default gromacs build. -Micholas === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center

Re: [gmx-users] Normal mode analysis

Yes I used double precision for everything. -Katrien From: Smith, Micholas D. Sent: woensdag 26 februari 2020 13:39 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Normal mode analysis Is your build of GROMACS using double

Re: [gmx-users] Listing residues in gromacs

Hi Christian, Thank you for your reply. The command worked well. I got the indices of the residues. I want to calculate the occupancies of the residues near my reference ion within say 0.5 nm. It will help me a lot if you could suggest something for it. I have tried gmx distance and gmx mindist

[gmx-users] Normal mode analysis

?Hello, Currently I am trying to perform a normal mode analysis on my pdb file using Gromacs 2019.3. But during energy minimalisation I can't seem te get my energy low enough. it remains around 10^01-10^00. I used the attached mdp-files. Am I doing something wrong? If so, what am I doing

Re: [gmx-users] Thesis developed software; which Open-source License?

Hi Henry, Although I'm not a lawyer here's how I understand it. You may want to check it with your department/university/company's legal department. I don't know anything about licensing data, but take a look at creative commons licenses if you want it to be open. See also:

Re: [gmx-users] Umbrella sampling of peptide-membrane system

Hi, Justin's tutorial is not a fully generalized procedure for umbrella sampling; it shows a workflow for one specific example which is not always applicable to other systems. In general, you don't have to use position restraints for anything in umbrella sampling. Justin uses them to keep the