[gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

Dear Gromacs users, I want to simulate Guanine ( a nitrogenous base) molecules in water using OPLS AA force field. I used the "opls aa" parameters from atomtypes.atp ((JACS,113,2810(1991)). on calculating the total charge of one molecule it comes to a negative value. dose it means that guanine

Re: [gmx-users] MDRUN crash

thank you for the advice justin! i have made some research and i use PME for electrostatics that i noticed it's pretty common. Unfortunately the mdrun this fatal error appeared: Program mdrun, VERSION 4.5.4 Source code file: pme.c, line: 538 Fatal error: 1629 particles communicated to PME node 4

Re: [gmx-users] MDRUN crash

Hi, Please don't start new work with old out-of-maintenance software, or at least use the most recent bug fix from that release branch. You should also do an equilibration with a normal acetone first, so that you know whether it's your equilibration or your shell model that is the problem. Mark

Re: [gmx-users] Basic Understanding about Gromacs C library

On 16/06/16 19:29, Murilo Kramar wrote: Greetings, List, I have a set of data that I used to analyze through VMD. As the set is quite heavy and there are many of them, using VMD was a bit cumbersome. So it has been decided that working in GROMACS would present benefits. The first step that I

Re: [gmx-users] MDRUN crash

On 6/17/16 3:56 AM, Luca Banetta wrote: Thank you for your support mark! I run an equilibration with a simple acetone molecule and it works with the mdp file i wrote in the first e-mail. I try to take a look at the shell to see if i made mistakes in its definition. Yes, the topology is wrong

Re: [gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

Dear Justin, I have already added the H to the guanine molecule striped from the nucleotide. The charges given in the ffnonbonded.itp for all the atoms of guanine (Including the H on N9) do not add to zero. *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical

Re: [gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

On 6/17/16 4:42 AM, Anurag Dobhal wrote: Dear Gromacs users, I want to simulate Guanine ( a nitrogenous base) molecules in water using OPLS AA force field. I used the "opls aa" parameters from atomtypes.atp ((JACS,113,2810(1991)). on calculating the total charge of one molecule it comes to

Re: [gmx-users] compile 2016-beta2 failed

Hi, Whatever cicc is, you look like you've changed the environment between when you started make and continued it. That's probably unwise. Also you made a spelling error in your install prefix, which you probably want to fix. Mark On Fri, Jun 17, 2016 at 8:38 PM Albert

Re: [gmx-users] compile 2016-beta2 failed

HEllo Mark: Thanks a lot for the reply. I replied Gromacs with the following command line: cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2 -DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-7.5 make -j32 But it still failed with messages: Building

[gmx-users] compile 2016-beta2 failed

Hello: I am trying to use the following command line to compile Gromacs-2016 beta2: CMAKE_PREFIX_PATH=/home/albert/install/gromacs/fftw-3.3.4 cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/romacs-2016-beta2 -DGMX_GPU=ON -DGMX_MPI=ON make -j32 but the make step failed with

Re: [gmx-users] compile 2016-beta2 failed

Hi, My earlier comments all stand - you need a working cuda compilation environment, and the people to help you do that are the people who installed it :-) Mark On Fri, Jun 17, 2016 at 9:52 PM Albert wrote: > Thanks a lot for such comments. > > I specified the path of

Re: [gmx-users] compile 2016-beta2 failed

Hi, You're going to need to talk to your cluster admin about how to get a working CUDA compilation setup. Once you have that, GROMACS will compile. Mark On Fri, Jun 17, 2016 at 8:56 PM Albert wrote: > HEllo Mark: > > Thanks a lot for the reply. > > I replied Gromacs with

Re: [gmx-users] compile 2016-beta2 failed

cicc is a cuda compiler (i.e., nvcc) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Albert Sent: 17 June 2016 14:55:02 To: gmx-us...@gromacs.org Subject: Re:

[gmx-users] (no subject)

Dear all, I have two peptide molecules at the surface of lipid bilayer. I want to apply position restrain on the reference peptide molecule at the surface and pull the other peptide. How to apply position restrain on COM of a peptide molecule and pull the other peptide by using

Re: [gmx-users] compile 2016-beta2 failed

Thanks a lot for such comments. I specified the path of cicc in my .bashrc as the following: export PATH=/opt/common/cuda-7.5/nvvm/bin:$PATH Then compiled it again cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2 -DGMX_GPU=ON -DGMX_MPI=ON

[gmx-users] SOLVED: Re: helixorient, jacobi iteration or junk output...?

Hi, OK after some messing around, it appears the bug is in the use of.xtc as input. I dumped the C-alpha atoms as a .pdb (using trjconv) and then the .ndx selection is "0 0". Seems to complete without crashing or the jacobi error. Now, we need to fix the .xvg format to be something useful.

[gmx-users] helixorient, jacobi iteration or junk output...?

Hi, I am trying to use helixorient to analyse my trajectories, using gromacs 5.0.2 It appears to fail on: Program gmx, VERSION 5.0.2 Source code file: /build/gromacs-dDhxvD/gromacs-5.0.2/src/gromacs/linearalgebra/nrjac.c, line: 163 If I allow it to process more than one frame. I have tried to

Re: [gmx-users] compile 2016-beta2 failed

HI Mark: But in my machine, all the file from cuda-7.5 development package has been installed. thanks again. On 06/17/2016 10:03 PM, Mark Abraham wrote: Hi, My earlier comments all stand - you need a working cuda compilation environment, and the people to help you do that are the

Re: [gmx-users] job failed. Too many CPU?

On 6/17/16 5:32 PM, Albert wrote: Hello: I am trying to run a Gromacs job with command line: mpirun -np 1 gmx_mpi grompp -f step6.0_minimization.mdp -o 60.tpr -n -c step5_charmm2gmx.pdb -maxwarn -1 mpirun -np 56 mdrun_mpi -s 60.tpr -g 60.log -c 60.gro >& 60.info I am using Charmm36 FF

Re: [gmx-users] compile 2016-beta2 failed

Hi, That's just one part of the puzzle, since you're also trying to use icc and MPI. Mark On Fri, Jun 17, 2016 at 10:16 PM Albert wrote: > HI Mark: > > But in my machine, all the file from cuda-7.5 development package has > been installed. > > thanks again. > > On

[gmx-users] job failed. Too many CPU?

Hello: I am trying to run a Gromacs job with command line: mpirun -np 1 gmx_mpi grompp -f step6.0_minimization.mdp -o 60.tpr -n -c step5_charmm2gmx.pdb -maxwarn -1 mpirun -np 56 mdrun_mpi -s 60.tpr -g 60.log -c 60.gro >& 60.info I am using Charmm36 FF for my system which contains 60,000

[gmx-users] Gromacs 5.1 - trouble with insert-molecules

Hi, I am upgrading from gromacs 4.6 to gromacs 5.1. Gromacs 4.6 had "genbox," which I was able to use without a problem. With gromacs 5.1, I am using insert-molecules to generate my initial configuration containing water, ethanol, and a lennard-jones particle which I defined. When I attempt to

Re: [gmx-users] compile 2016-beta2 failed

On 6/17/16 4:15 PM, Albert wrote: HI Mark: But in my machine, all the file from cuda-7.5 development package has been installed. Have you tried compiling without -j32? In my experience, trying to use too many cores to compile leads to unpredictable failures, like files failing to be

Re: [gmx-users] Checksum and .log error

Hi Grommunity, It seems like the runs have finished at different stepswould this call the error? Best Teresa On 2016-06-16 22:04, Mark Abraham wrote: Hi, Mdrun is reporting that your entire file can't be read, which likely means that something a out the filsystem or the way you are

Re: [gmx-users] MDRUN crash

Thank you for your support mark! I run an equilibration with a simple acetone molecule and it works with the mdp file i wrote in the first e-mail. I try to take a look at the shell to see if i made mistakes in its definition. Il 17/Giu/2016 08:47, "Mark Abraham" ha

Re: [gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

On 6/17/16 6:26 AM, Anurag Dobhal wrote: Dear Justin, I have already added the H to the guanine molecule striped from the nucleotide. The charges given in the ffnonbonded.itp for all the atoms of guanine (Including the H on N9) do not add to zero. As I said, those charges mean nothing.

Re: [gmx-users] Total Charge on Guanine molecule by OPLS AA force field is negative

Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Fri, Jun 17, 2016 at 5:02 PM, Justin Lemkul wrote: > > > On 6/17/16 6:26 AM, Anurag Dobhal wrote: > >> Dear Justin, >> >> I have

Re: [gmx-users] MDRUN crash

thank you for your great useful help justin! I have just written two directives in which I declare polarization and exlusions as you wrote me on the previous e-mail [ polarization ] ; Vsite shell functiontype alpha nm^3 11 1210.001 [ exclusions ] ; 4 1

Re: [gmx-users] MDRUN crash

On 6/17/16 7:52 AM, Luca Banetta wrote: thank you for your great useful help justin! I have just written two directives in which I declare polarization and exlusions as you wrote me on the previous e-mail [ polarization ] ; Vsite shell functiontype alpha nm^3 11 12