Re: [gmx-users] compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition

--enable-shared 1086 make 1087 make install The only difference is that I delete the option of --enable-long-double for compiling fftw and add the option of --enable-shared for compiling gromacs. Thanks all for the suggestions. All the best. Qinghua Liao On Wed, Mar 27, 2013 at 2:04 PM

Re: [gmx-users] compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition

compilation of fftw 3.3, but not for compilation of gromacs 4.5.4. Problem remains unsolved. I choose this old version is to keep the simulations consistent with previous simulations. Thanks for the suggestion! All the best, Qinghua Liao On Wed, Mar 27, 2013 at 12:59 PM, Justin Lemkul wrote: > >

[gmx-users] compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition

red option. Could someone give me some suggestions to help me this out? Any reply will be appreciated. All the best, Qinghua Liao -- Best Regards, Qinghua -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archiv

[gmx-users] simulations in vacuum in parallel

Dear gmx users, I tried to do simulations of a small peptide in vacuum, I found that it failed to be run in parallel, even when I use only 8 cores. My system only have hundreds of atoms. the problem may be resulted from domain decomposition. When I choose particle decomposition method, for small s

[gmx-users] distance restraints fails

Dear gmx users, I tried to apply distance restraints to my system, but I found that it failed because the distance between the restraints atoms in the last frame is bigger than what we want. Here are the parameters for distance restraints in the topology file: [ distance_restraints ] ; ai aj ty

[gmx-users] develop parameters for small molecules

Dear GMX users, We want to develop the ff parameters for some small molecules in consistent with gromos 53a6, and I know that PRODRG can do it, but it is not accurate enough. So we want to do some QM calculations to validate it. However, how can I derive these parameters for bonds and dihedrals fr

[gmx-users] Re: gmx-users Digest, Vol 92, Issue 44

the Opt or EnGrad keyword. Hope that helps, Christoph On 12/08/2011 11:43 AM, Qinghua Liao wrote: > Dear GMX users, > > Could someone give me some suggestions on how to set the BASENAME file > in the QMMM simulations using gromacs/orca? Is the BASENAME file the > inp file in orca? Th

[gmx-users] how to set the BASENAME in QMMM simualtions using gromacs/orca

Dear GMX users, Could someone give me some suggestions on how to set the BASENAME file in the QMMM simulations using gromacs/orca? Is the BASENAME file the inp file in orca? Thanks very much! Best Regards, Qinghua -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mail