Re: [gmx-users] converting amber distributed parameters to gromacs.

Could you please tell how do i use this script over amber file? Thanks. On Wed, Nov 7, 2012 at 5:58 PM, Felipe Pineda, PhD < luis.pinedadecas...@lnu.se> wrote: > ffamber.cnsm.csulb.edu/**amb2gmx.pl<http://ffamber.cnsm.csulb.edu/amb2gmx.pl> > > > > On 11/07/2012 0

Re: [gmx-users] Re: mpi enabled gromacs (

Thanks for your reply. Actually, i have installed gromacs in my cluster and then i configured with --enable-mpi --program-suffix=_mpi* *option by following make mdrun, make install-mdrun. It installed nicely and does works well. I want to know how would i check whether mpi works in gromacs? Is ther

Re: [gmx-users] mpi enabled gromacs

eed to recompile your mpi library with that option. At least > that is what I did last time when I install GROMACS. > On Oct 22, 2012 5:04 PM, "Rajiv Gandhi" wrote: > > > Dear Gromacs users, > > > > I have been trying to install mpi enabled gromacs in my clus

[gmx-users] Error on mpi installation

Dear Gromacs, I am trying to install gromacs with mpi enabled in my cluster and i end up with following error: libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error I can able to install gromacs i

Re: [gmx-users] Dipole moment

Dear Gromacs, I am trying to install gromacs with mpi enabled in my cluster and i end up with following error: libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or unhandled argument `../mdlib/libmd_mpi.la' make[1]: *** [libgmxpreprocess_mpi.la] Error I can able to install gromacs i

Re: [gmx-users] How to produce the photodissociation in Gromacs?

Could you tell me what is the procedure to cut the bond to produce the photodissociation? On Thu, Sep 20, 2012 at 3:12 PM, Mark Abraham wrote: > On 20/09/2012 1:08 PM, Rajiv Gandhi wrote: > >> Dear all, >> >> Why all people cut the protein ligand bond to produce

Re: [gmx-users] Resuming of calculation from last *.cpt

Dear all, I have read few papers regarding the photo dissociation event such as Myoglobin heme-ligand bond deletion to induce the photodissociation in MD simulation. Could you please tell me the procedure how can i perform the photodissociation mechanism in Gormacs and which force field have to u

[gmx-users] Calculating secondary structure movements

Dear all, I would like to measure the rotation angle of helix movement during MD simulation course. Can you tell me how can I measure and make that rotation angle plot ? Thanks. Regards Rajiv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-user

[gmx-users] Calculating number of water molecules involves between dimer protein.

I want to calculate the time dependence of the average number of interfacial water molecules in dimer protein ( example hemoglobin), In experimental results proposed that the water molecules get increase/decrease on time scale manner. Is't possible to show up this process in MD simulation studies.

Re: [gmx-users] Hydrogen bond breaking process

owledge on this, Thanks in advance. On Mon, Sep 3, 2012 at 2:51 PM, Peter C. Lai wrote: > Well there is always ReaxFF. You'd still have to use QM/MM to parameterize > the various states though. > > On 2012-09-02 09:48:25PM -0400, Justin Lemkul wrote: > > > > &g

Re: [gmx-users] Hydrogen bond breaking process

n 8/31/12 10:43 PM, Rajiv Gandhi wrote: > >> Can you tell me "how to predict the Hydrogen bond breaking process (For >> example Fe-CO hydrogen bond broken in Myoglobin at 100 ps) through MD >> simulation? >> >> > There is no hydrogen bonding in a Fe-CO inter

[gmx-users] Hydrogen bond breaking process

Can you tell me "how to predict the Hydrogen bond breaking process (For example Fe-CO hydrogen bond broken in Myoglobin at 100 ps) through MD simulation? Kind regards Rajiv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the