Re: [gmx-users] problem with chimera opening gromacs 4.6.5 trajectories

Which Chimera version are you using? Have you tried the latest (at least 1.8)? http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.8.html : support added for Gromacs 4.6 trajectories Nicolas 2014-04-23 14:02 GMT-04:00 Rafael I. Silverman y de la Vega rsilv...@ucsc.edu: Hi all I have been having

[gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)

Dear all, I am joining a project where people are using the CHARMM22 force field. They converted a .prmtop file from Amber to Gromacs format with acpype. In the output topology, there are no Urey-Bradley potentials or improper dihedrals (for example, all the [ angle ] functions are of type 1 and

[gmx-users] Unified topology

Dear all, Someone gave me a topology file for a system which was converted from Amber (with the CHARMM27 force field). When I compare (via a single point) with a topology coming from pdb2gmx, I find some differences between the energetic values. I would like to find the cause. The topology from

Re: [gmx-users] Confusion on improper dihedrals and Urey-Bradley (lost when converting from Amber with acpype)

etails about it in > https://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx > > Alan > > On 9 October 2015 at 12:39, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 10/8/15 11:48 AM, Nicolas Cheron wrote: > > > >> Dear all, > >&g

[gmx-users] Gromacs and Gcc5.2

Dear all, I am wondering if there is an official statement regarding compiling Gromacs with gcc5.2.0 (or any gcc from the 5.x branch). Is it recommended or not? Should we expect improvements? I have tried quickly some small benchmarks (with Gromacs 4.6.3 and Gromacs 5.1) and found improvement on

Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3

romacs-5.1.1/build/CMakeFiles/CMakeError.log". Nicolas 2016-01-24 22:29 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>: > > Hi, > > That shouldn't happen. What does the terminal output when you run cmake in > a clean build tree? > > Mark > > On Sun, 24 Jan

Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3

> Koji > > On Mon, Jan 25, 2016 at 12:56 PM, Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Hi, > > > > All my installations are made from a clean build directory. I am > > using CentOS release 6.6 and the CPU is Intel Xeon CPU E5-2650

Re: [gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3

Hi, I have faced the same problem, with gcc 4.8.3, 4.9.1 and 5.2. I ended up asking for SIMD=AVX_256. So I assume there is something else going wrong. Nicolas 2016-01-24 20:59 GMT+01:00 Mark Abraham : > Hi, > > Like the *5.1* installation instructions and that error

[gmx-users] Roadmap for new features

Dear all, Is there a place where the planned/hoped new features of Gromacs are listed? I am wondering if there is a chance that EVB, HREX (without the need to use plumed) or new QM/MM interface will be available at some point. I know that the developers are busy, but I am wondering what is in

[gmx-users] Regression test 4.6.7

Dear all, I am looking for the file regressiontests-4.6.7.tar.gz. I can't find it online, the previous links are done. Can someone please either send it to me or tell me where to find it? Thanks a lot. Nicolas -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

See: https://groups.google.com/forum/#!topic/plumed-users/eJ0xpnHPb_s and https://github.com/GiovanniBussi/plumed2/tree/v2.2-hrex Nicolas 2016-04-02 12:09 GMT+02:00 Mark Abraham : > Hi, > > On Fri, Apr 1, 2016 at 11:39 PM Christopher Neale < >

[gmx-users] Charmm topologies for DHF/NADPH

Dear all, I am searching for topology files in Gromacs format for the NADPH cofactor and the dihydrofolate (DHF) ligand that would be compatible with the Charmm27 force field. Does anyone here have them and woud kindly accept to send them to me? If you have them in another format than Gromacs, I

Re: [gmx-users] HID error in amber14sb.ff

Hi, I had this problem and wrote to Viet Man who uploaded the force field. I am quoting his answer: I have found the error come from HIP residues, diheral angle CB-CG-CD2-ND1 (= CT-CC-CW-NA). It causes by missing the improper dihedral angle information. To solve it, you may open file

[gmx-users] gmx select

Dear all, I am a little bit lost with the use of select. I am looking at a protein in a water:glycerol mixture. I would like to count how many glycerol molecules there are within 3Angstrom of the protein. I first used the following command to count the central atom (named C2): gmx select -s

[gmx-users] Use of gmx select

Dear all, I am a little bit lost with the use of select. I would like to count how many water molecules there are within 3Angstrom of a protein. I first used the following command to count the oxygen atoms: gmx select -s File.gro -f File.xtc -n Index.ndx -os Wat-0.3.xvg -xvg none -select "name

[gmx-users] Extension on different machines (CPU/GPU

Dear all, I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. I then wanted to extend the simulation to 300ns, and copied the .tpr and the .cpt to another machine with GPUs (also running Gromacs 5.1.2). I observed strange results, so I decided to also extend the simulation

Re: [gmx-users] Extension on different machines (CPU/GPU

clusions are valid > reflection of reality. > > Mark > > On Tue, Jun 5, 2018 at 10:37 AM Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Dear all, > > > > I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. > I >

[gmx-users] Periodic saving of checkpoint file

Dear all, I would like to run a long NVT simulation and save a checkpoint file every 10ps (in order to then run short NVE simulations from each checkpoint). Is there a way to save a .cpt file every 10ps in an automatic way? I can do it with other program, for example with Amber "ntwr=-5000" will

Re: [gmx-users] Periodic saving of checkpoint file

grompp -e -t along with the > regular inputs. > > Mark > > On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron < > nicolas.cheron.bou...@gmail.com> wrote: > > > Dear all, > > > > I would like to run a long NVT simulation and save a checkpoint file > every > &g

Re: [gmx-users] Calculation of RMSF

Thank you for your answer. As Mala said, since it is called the reference structure, I was thinking that the RMSF was computed with respect to this structure and not the average structure. Is there any way with Gromacs to compute RMSF exactly with respect to a given structure? If I want to study

Re: [gmx-users] solute tempering (REST2)

Hi, You can patch Gromacs with Plumed and use hrex: * generate a full .top file of your system (with -pp in the grompp command) * open your .top and add "_" in the second column (type) of each atom you want to apply REST2 in the [ atoms ] section of the moleculetype * use the command "plumed