[gmx-users] Sulfate ion parameters

Dear gromacs users, I wanted to simulate sulphate ions in water using oplsaa force field but I couldn't find parameters for sulphur and oxygen atoms of sulphate ions in the oplsaa force field files. Can anyone suggest from where can I get these parameters? Charmm force field has the

[gmx-users] modeling CNT, center of mass velocity, energy minimization

Hi GROMACS users,  I have some questions:  1-  Can I model a carbonnanotube (CNT) conveying fluid in GROMACS subjected to a magnetic field?2-  How can I check the centerof mass velocity of my system?3-  I want to calculate volumeand water self diffusion coefficient

[gmx-users] recompile gromacs 5.0.7

Respected sir! Thanks for your response I recompile my system(gromacs5.0.7) but the error remain same. looking for your response to solve this issue. thank you one again -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] pdb2gmx generate .itp file for each molecule

Hi , Maybe you can try -merge all when using pdb2gmx. -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] pdb2gmx generate .itp file for each molecule

​Hi, gmx users, I used materials studio to generate a .pdb file containing 160 PTFE chains, and then modified the oplsaa forcefiled as Justin did. The pdb2gmx generated right .gro and .top files. But the problem is that it generated one .itp file for each molecule. Since there are 160 identical

[gmx-users] Question about WHAM

Hello,This question is more about the WHAM technique in general, but I take the liberty to ask it in this forum, hoping somebody can point me in the right direction. I am calculating the free energy difference between two wells separated by an energy barrier using an umbrella potential

Re: [gmx-users] protein atoms with alternate conformations

Thanks :) In case anyone else wonders, the highest occupancy atom is taken. Irem > On Feb 23, 2016, at 3:04 PM, Mark Abraham wrote: > > Hi, > > Swap them and see :-) > > Mark > > On Tue, 23 Feb 2016 20:55 Irem Altan wrote: > >> Hi, >> >> I

Re: [gmx-users] protein atoms with alternate conformations

Hi, Swap them and see :-) Mark On Tue, 23 Feb 2016 20:55 Irem Altan wrote: > Hi, > > I have a protein that contains atoms with alternate conformations: > > ATOM856 SG ACYS A 217 7.649 52.725 28.525 0.58 12.64 >S > ATOM859 SG BCYS A 217 7.282

[gmx-users] protein atoms with alternate conformations

Hi, I have a protein that contains atoms with alternate conformations: ATOM856 SG ACYS A 217 7.649 52.725 28.525 0.58 12.64 S ATOM859 SG BCYS A 217 7.282 54.809 26.839 0.42 15.97 S How does pdb2gmx handle this? I checked the .gro file to see that

Re: [gmx-users] Protein-ligand system simulations with GROMACS

Hi, These questions are quite specific to your problem. There's no way we can predict what equilibration time will suffice for your system. Your simulation time also depends on what the aim of your simulations is and what you hope to observe. That said, current simulations are generally a couple

[gmx-users] Protein-ligand system simulations with GROMACS

Dear colleagues, I'm starting to use GROMACS and I'm simulating a system between an RNA binding protein and a small RNA ligand (a dinucleotide, ~60 atoms) in a cubic box. I set AMBER99SB-ILDN protein, nucleic AMBER94 as a forcefield, with a tip3p water model. This was only to put you in

Re: [gmx-users] Segmentation fault during equilibration

Hi, As normal, even for coarse-grained simulations, equilibration may require bigger rearrangements for some starting conditions than others. The usual advice for http://www.gromacs.org/Documentation/Terminology/Blowing_Up still applies - particularly to try smaller time steps while relaxing what

[gmx-users] Segmentation fault during equilibration

Hi all, I am running an equilibration of a membrane/protein coarse grained system and got this Segmentation fault error. --- Reading file equilibration.protein_DPPC.tpr, VERSION 4.6.5 (single precision) Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this

Re: [gmx-users] Huge conformational change of ATP molecules

Hi, Indeed that seems to short. So if one has excluded natural processes, the artificial ones remain the only possible ones... Your process does have to include a custom index group, for example... see http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark On Tue,

Re: [gmx-users] Huge conformational change of ATP molecules

Hi Mark, Thank you for the suggestions, but I don't think it is because of the PBC artifacts. I do centered my protein and ligand with "-center -pbc mol" option. The protein itself looks fine without any breaking. It's just the ATP that moves out and stays at the outer surface of the protein. I

Re: [gmx-users] confusion on energy for a system of protein sovated in water

On 2/22/16 10:03 PM, Ming Tang wrote: Thanks Justin, How about LJ and Coulomb energy? I want to see the trend of protein energy only. I defined 2 energy group: protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein option when using g_energy. Are they VDW and Coulomb

Re: [gmx-users] gmx sasa versus g_sas

On 2/23/16 9:45 AM, Sara Del Galdo wrote: Hi Gromacs users, I am using gromacs tool g_sas to calculate protein excluded volumes and I noticed that it provides significant different excluded volume values when compared to the new version gmx sasa tool. Does anyone know the reason of this and

[gmx-users] gmx sasa versus g_sas

Hi Gromacs users, I am using gromacs tool g_sas to calculate protein excluded volumes and I noticed that it provides significant different excluded volume values when compared to the new version gmx sasa tool. Does anyone know the reason of this and which of the two tool is more reliable? Thanks

Re: [gmx-users] Regarding installation problem

Hi, That's still going to need an updated binutils, though. Mark On Tue, Feb 23, 2016 at 3:40 PM Szilárd Páll wrote: > AVX is supported even by gcc 4.4.7 (although admittedly I'm not sure if > it's functional), so you may want to try -DGMX_SIMD=AVX_256, that will >

Re: [gmx-users] Regarding installation problem

AVX is supported even by gcc 4.4.7 (although admittedly I'm not sure if it's functional), so you may want to try -DGMX_SIMD=AVX_256, that will waste your hardware a bit less. -- Szilárd On Tue, Feb 23, 2016 at 3:02 PM, Mark Abraham wrote: > Hi, > > You can probably

Re: [gmx-users] Regarding installation problem

Hi, You can probably use any GROMACS version, if you want it to run slowly and generate less science for you. Just use cmake -DGMX_SIMD=SSE4.1. Mark On Tue, Feb 23, 2016 at 2:47 PM SOUVIK MONDAL wrote: > Which version of gromacs will be suitable for gcc version 4.4.7? >

Re: [gmx-users] Regarding installation problem

Which version of gromacs will be suitable for gcc version 4.4.7? - Original Message - From: "Mark Abraham" To: gmx-us...@gromacs.org Sent: Tuesday, February 23, 2016 6:05:13 PM Subject: Re: [gmx-users] Regarding installation problem Hi, The simplest thing is

Re: [gmx-users] Regarding installation problem

Hi, The simplest thing is to get the latest version of gcc that your operating system (e.g. Linux distribution) supports. Sadly, people often sell compute systems based on "mature, stable, reliable" versions of software, but with modern hardware, which automatically means that everything is out

Re: [gmx-users] Regarding installation problem

Can u tell what are compilers I need to up-to-date? - Original Message - From: "Mark Abraham" To: gmx-us...@gromacs.org Sent: Tuesday, February 23, 2016 4:50:52 PM Subject: Re: [gmx-users] Regarding installation problem Hi, On Tue, Feb 23, 2016 at 11:54 AM

Re: [gmx-users] Regarding installation problem

Hi, On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL wrote: > After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > the output in that ternimal comes as follows > > - The C compiler identification is GNU 4.4.7 > -- The CXX compiler identification is

Re: [gmx-users] Regarding installation problem

After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON the output in that ternimal comes as follows - The C compiler identification is GNU 4.4.7 -- The CXX compiler identification is GNU 4.4.7 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler:

Re: [gmx-users] Regarding installation problem

Hi, Yes, I know. That's its job. The only likely relevant part is very near the end. But first I wanted to see the terminal output - what you saw on the screen when you ran cmake. Mark -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Regarding installation problem

The CmakeErroor.log file have following things Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following output: Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp Run Build Command:"/usr/bin/gmake" "cmTC_bf3f2/fast" /usr/bin/gmake -f

[gmx-users] Post-doctoral position in Computational Physics

Hi all, A post-doctoral position in Computational Physics is currently available in the Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab (https://beta.iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems) at IIT - Genoa (ITA) to work on

[gmx-users] generating an initial structure with a gromacs compatible tool

Hi all, Is there a friendly Gromacs compatible tool for generating a .gro/.pdb file using a specific forcefield topology specification within Gromacs itself? For context: I¹m in the process of fully parameterising five custom protein residues for the amber forcefield from ab initio calculations.

Re: [gmx-users] Effect of compilers loaded at runtime

Hi, Very likely not, but technically the answer can depend how the compiler toolchain sets up things like dynamic loading of libraries. You can perhaps explore that effect with the command line tools ldd and objdump on the gmx executable. You could read the Intel docs, but they'll just say "yes

Re: [gmx-users] Huge conformational change of ATP molecules

Hi, It sounds like you are observing artefacts from http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan wrote: > Hi Gromacs Users, > > I'm running 20ns MD simulation of a protein kinase with ATP

Re: [gmx-users] Mdrun with rdd option

Hi, On Tue, Feb 23, 2016 at 6:25 AM Raju Lunkad < r.lun...@students.iiserpune.ac.in> wrote: > Dear Gromacs users, > I am trying to run a simulation but I am getting the error regarding the > domain decomposition. Which error? People often can't help much without precise information. Probably

Re: [gmx-users] Regarding installation problem

Hi, The limited information you've provided doesn't sound like it is the real problem. What does the whole cmake terminal output say? Mark On Tue, Feb 23, 2016 at 7:38 AM SOUVIK MONDAL wrote: > Hi > I have found the following problem regarding gromacs 5.1.2