Re: [gmx-users] Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values

Hi, You need to specify a group, eg System. That this is not the default behavior protects you from making a typo and accidentally coupling the whole system when it was not your intent. Mark On Thu, Jul 12, 2018, 17:24 Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: >

Re: [gmx-users] Making group of different atoms

In the index editor of make_ndx does "a 1566 1567 1569 1571 1574 1579" not work? Alternatively, you can just manually make the index file as Sohaib suggested. An index group is just: [ name_of_group ] ;atomnr of atoms that make up the group eg. 1566 1567 1569 1571 1574 1579 etc.. On 12 July 2018

Re: [gmx-users] Making group of different atoms

Yes, I have tried but I am having trouble in making a group for atoms with different numbers. On Wed, 11 Jul 2018, 22:29 Quyen V. Vu, wrote: > Have you try make_ndx tool of Gromacs? > > On Wed, Jul 11, 2018, 00:09 Chetan Puri wrote: > > > Can someone guide me in how to make a group for atoms

[gmx-users] Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values

Dear Gromacs users, I am trying to perform a NVT equilibration. However, I obtain this error: Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values I don't understand the problem because I don't have defined any group, I am indicating the ref-t and tau-t for the

Re: [gmx-users] rerun from random seeds

Yes, this will generate velocities with a random seed. -- Szilárd On Thu, Jul 5, 2018 at 5:15 PM MD wrote: > Hi Gromacs folks, > > I am trying to re-run a 100 ns simulation with different velocities and > random seed. Would the setup from the mdp file as the following a good one? > > ;

Re: [gmx-users] pme grid with gpu

That's the PP-PME load balancing output (see -tunepme option / http://manual.gromacs.org/documentation/2018/user-guide/mdrun-performance.html ). -- Szilárd On Tue, Jul 10, 2018 at 7:35 PM Mahmood Naderan wrote: > Hi, > When I run mdrun with "-nb gpu", I see the following output > > >

Re: [gmx-users] cpu threads in a gpu run

On Tue, Jul 10, 2018 at 5:12 AM Mahmood Naderan wrote: > No idea? It seems to be odd. At the beginning of run, I see > > NOTE: GROMACS was configured without NVML support hence it can not exploit > application clocks of the detected Quadro M2000 GPU to improve > performance. >

Re: [gmx-users] cpu threads in a gpu run

On Mon, Jul 9, 2018 at 12:43 PM Mahmood Naderan wrote: > Hi, > When I run "-nt 16 -nb cpu", I see nearly 1600% cpu utilization. You request the CPU to do the work, so all cores are fully utilized. > However, when I run "-nt 16 -nb gpu", I see about 600% cpu utilization. The default

Re: [gmx-users] GROMACS- suggestion for GPU buying

If price does not matter, get V100s; if it matters somewhat get TITAN-V's. Same applies if you want best performance per simulation. If you want best perf/buck, the 1080 Ti is still better investment (or you could wait an see if the next-gen consumer cards come out soon). -- Szilárd On Tue, Jul

Re: [gmx-users] REPOST Coarse graining carbon nanotubes and MARTINI

Hi Raman, I forwarded your question to some people off list, and chance has it I just got a reply back! So with a big thanks to R. Alessandri and M. Vögele! Peter Hi, 1.)  We made a tool to create Martini models for open carbon nanotubes:  https://github.com/bio-phys/cnt-martini. The

[gmx-users] REPOST Coarse graining carbon nanotubes and MARTINI

Dear All, I have earlier posted the below email but received no reply. I am reposting it and will be thankful if someone can help me out. Regards, Raman On Jul 6, 2018 3:02 PM, Raman Preet Singh wrote: > > Dear All, > > > I want to run a CG simulation of carbon nanotubes (CNTs) and different

[gmx-users] Commented atoms in [pair] list

Dear Gromacs users, Recently, I downloaded some simulation files from a web site (their work is already published). Once I checked their itp files, I saw that they commented some atoms in [pair] list. I would like to know what could be the reason for that? Thank you.  -- Gromacs Users mailing

Re: [gmx-users] Dihedral between non bonded atoms

Hi, The list cannot accept attachments, so please find another way to share your inputs, e.g. a file sharing service. The pdb on its own would not be enough for anyone to help, because that doesn't tell us what atoms are concerning you. By design, pdb2gmx will not try to generate a dihedral if

[gmx-users] Time correlation function computation

Dear All, How to find time correlation function of the vectors formed by Cα of a protein in molecular dynamic simulation? Thank You. -Abantika -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Dihedral between non bonded atoms

Hi, is there a reason why gromacs demands parameters for dihedral angles that are not bonded? For example i,j, and k are bonded but l is not. The distance of k and l is about 2.7 Angstroem. How can i tell gromacs to ignore these dihedrals during pdb2gmx. I did no define a bond in the .rtp

[gmx-users] Membrane simulation analysis - membrane thickness and area per lipid

Hello, I am running some CGMD simulations of a membrane protein embedded in a model of E. coli membrane (12x12 nm bilayer with different lipids), and I want to do the analysis of the membrane thickness and area per lipid (APL). For these tasks I am comparing the performance of FATSLiM,

Re: [gmx-users] Convergence of systems.

there are various properties you can check such as potential energy, RMSD, Temperature ... On Thu, Jul 12, 2018 at 2:19 PM SHYANTANI MAITI wrote: > Dear all, > How to determine whether the system converges or not in molecular dynamics > simulation? > > -- > Best regards, > *Shyantani Maiti* >

[gmx-users] Convergence of systems.

Dear all, How to determine whether the system converges or not in molecular dynamics 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