[gmx-users] Ligand Topologies

Dear Users, I am trying to do Protein-Ligand MD simulations using GROMACS. I have tried to build topology files of my ligands using external tools like PRODRG server. I tried to correct the charges in line with Dr. Justin's paper *Practical Considerations for Building GROMOS-Compatible Small-Molec

Re: [gmx-users] Ligand Topologies

Find out why your charge is not integral! Read all the output of whatever tool built the .itp file and reconsider your choices. Mark On Mon, Sep 9, 2013 at 9:46 AM, MUSYOKA THOMMAS wrote: > Dear Users, > I am trying to do Protein-Ligand MD simulations using GROMACS. I have tried > to build topol

Re: [gmx-users] GaussView 4.0 and ITP adjuster

Hmmm GaussView is a supplement to Gaussian to prepare input files and visualize some (but far not all) results. Of course, it has nothing to do with gromacs and its topologies. Or, do I misunderstand you? Dr. Vitaly V. Chaban On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS < mutemibiochem

Re: [gmx-users] GaussView 4.0 and ITP adjuster

Hi Dr, Check that link and see the role of GaussView in GROMACS. Thank you. http://www.hindawi.com/journals/chem/2013/803151/ On Mon, Sep 9, 2013 at 12:46 PM, Dr. Vitaly Chaban wrote: > Hmmm > > GaussView is a supplement to Gaussian to prepare input files and visualize > some (but far not al

Re: [gmx-users] GaussView 4.0 and ITP adjuster

"First we built their 3D structures in the *.pdb format using Gauss View 4.0 and Frisch et al. [30] and submitted them to energy minimization with Frisch et al. [30] using the algorithm B3L

[gmx-users] intermittent changes in energy drift following simulation restarts in v4.6.1

Dear All, I've been analysing a series of long (200 ns) NVE simulations (md integrator) on ~93'000 atom systems I ran the simulations in groups of 3 using the -multi option in gromacs v4.6.1 double precision. Simulations were run with 1 OpenMP thread per MPI process The simulations were res

Re: [gmx-users] intermittent changes in energy drift following simulation restarts in v4.6.1

Sounds worrying :-( Thanks for the detailed report and trouble-shooting! So far, I can't think of a reason for it. A couple of suggestions: * try again with 4.6.3 (at least while trouble-shooting) in case its a fixed bug * post a representative .mdp file * is there anything out of the ordinary in

Re: [gmx-users] intermittent changes in energy drift following simulation restarts in v4.6.1

Hi Mark, Thanks for the quick response, On 09/09/13 15:45, Mark Abraham wrote: Sounds worrying :-( Thanks for the detailed report and trouble-shooting! So far, I can't think of a reason for it. A couple of suggestions: * try again with 4.6.3 (at least while trouble-shooting) in case its a fixe

RE: [gmx-users] g_current

Hi, as I just recently left the university and started to work in industry, there are currently a lot of things to be done. However, I will still try to contribute to GROMACS as good as possible. Next week there will be some time left in the evening and I will report back ASAP. /Flo > -Orig

Re: [gmx-users] intermittent changes in energy drift following simulation restarts in v4.6.1

No obvious problems. Please open an issue at redmine.gromacs.org when you have something reproducible, but don't hurry, nobody's likely to have time to check it out for a week or two. Cheers, Mark On Sep 9, 2013 5:11 PM, "Richard Broadbent" < richard.broadben...@imperial.ac.uk> wrote: > Hi Mark,

Re: [gmx-users] NMR restrained MD

Ok..I got it Thanks Justin... --Rama On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti < ramkishn...@gmail.com> wrote: > > Hi Justin , > > I prepared .rtp files for lipid. what is the exact command to merge two > chains in gromacs. > > > > > On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul

Re: [gmx-users] NMR restrained MD

Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul wrote: > > > On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: > >> H >> i Justin, >> >> Thanks for your reply. >> >> >> How to do that? >> >>

[gmx-users] segfault on Gromacs 4.6.3 (cuda)

Dear GMX users, I recently compiled Gromacs 4.6.3 with CUDA (Intel compiler 11.x, SSE2, and CUDA SDK 5.0.35). I was doing a test run with simply 'mdrun -deffnm eq2_npt_verlet' (letting mdrun figure out what to use). I received the error telling me my graphics driver was older than the CUDA SDK, an

Re: [gmx-users] segfault on Gromacs 4.6.3 (cuda)

HI, First of all, icc 11 is not well tested and there have been reports about it compiling broken code. This could explain the crash, but you'd need to do a bit more testing to confirm. Regading the GPU detection error, if you use a driver which is incompatible with the CUDA runtime (at least as h

Re: [gmx-users] NMR restrained MD

Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. Thanks --Rama On Mon, Sep 9, 2013 at 4:43 PM, Justin Lemkul wrote: > > > On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote: > >> Hi Justin, >> >> I merge two molecu

Re: [gmx-users] NMR restrained MD

Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of errors. Thanks --Rama On Mon, Sep 9, 2013 at 1:57 PM

Re: [gmx-users] NMR restrained MD

On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for s

Re: [gmx-users] NMR restrained MD

On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote: Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of error

Re: [gmx-users] segfault on Gromacs 4.6.3 (cuda)

Hi Szilard, Thanks again for getting back. You may remember the previous thread I started on regression test failure with icc 11.x compiled binary. Falling back to SSE2 is my solution, and binaries compiled this way are able to pass all regression tests, including the one with GPU switched on. How

[gmx-users] Fwd: installing Gromacs4.6.3 on cygwin

Dear all I am installing gromacs -4.6.3 on cygwin with following commands tar -xvzf gramcs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_DOUBLE=on It runs fine and write file in build directory. when I run make command it gives following error. [ 15%] B