[gmx-users] negative dihedral cp (during cgenff conversion)

Random noob question: Should the cp field (field 7) in [ dihedraltypes ] always be positive or can it be negative? In the CGenFF conversion, the CHARMM dihedral has: OG302 CG2O2 CG321 CG331 -0.1500 1 180.00 ! LIPID methyl proprionate when I convert to gromacs: [ dihedraltypes ] ; i

[gmx-users] Compute Intensive benchmarks for Gromacs

Dear All, I would like to use Gromacs on a cluster of machines. I am not aware for technicalities of Gromacs, but I am looking for large problem size which can utilize my cluster resources, and should be able to create enough imbalance in the computations. The purpose is for bench-marking the clus

Re: [gmx-users] how to simulate a line charge

Amit Choubey wrote: sorry i did not mention it but the E field contribution should be zero, i am sure about it. Also when i make all the cutoff = 0 the energy terms are Step Time Lambda 00.00.0 Energies (kJ/mol)

Re: [gmx-users] how to simulate a line charge

sorry i did not mention it but the E field contribution should be zero, i am sure about it. Also when i make all the cutoff = 0 the energy terms are Step Time Lambda 00.00.0 Energies (kJ/mol) Bond Angle

Re: [gmx-users] how to simulate a line charge

Amit Choubey wrote: Following is the mdp file cpp = /usr/bin/cpp ;define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1 ; ; Energy minimizing stuff ; emtol = 200 emstep = 0.01

Re: [gmx-users] how to simulate a line charge

Following is the mdp file cpp = /usr/bin/cpp ;define = -DFLEX_SPC constraints = none integrator = steep nsteps = 1 ; ; Energy minimizing stuff ; emtol = 200 emstep = 0.01 pbc = no nstcomm

Re: [gmx-users] how to simulate a line charge

Amit Choubey wrote: Justin, when i define the whole line charge as a charge group i do get a coulomb energy contribution. I thought there would be no non-bonded contribution. I use a very high cut-off (longer than chain length) and no pbc. Am i missing something ? Without seeing your .mdp

Re: [gmx-users] how to simulate a line charge

Justin, when i define the whole line charge as a charge group i do get a coulomb energy contribution. I thought there would be no non-bonded contribution. I use a very high cut-off (longer than chain length) and no pbc. Am i missing something ? On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey wrote:

Re: [gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program

I used the newest version of gromacs 4.5.4 (and not install beta gpu version ) so everything goes well. thanks for your reply On Sun, Aug 14, 2011 at 5:52 PM, Justin A. Lemkul wrote: > > > H.Ghorbanfekr wrote: > >> Hi , >> >> I'm using mdrun-gpu for testing gpubench demos. >> But I've got this

Re: [gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program

H.Ghorbanfekr wrote: Hi , I'm using mdrun-gpu for testing gpubench demos. But I've got this error message: Fatal error: reading tpx file (topol.tpr) version 73 with version 71 program I installed different version of gromacs 4.5 to 4.5.4 and gpu-gromacs-beta 1, 2 versions. But it still d

[gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program

Hi , I'm using mdrun-gpu for testing gpubench demos. But I've got this error message: Fatal error: reading tpx file (topol.tpr) version 73 with version 71 program I installed different version of gromacs 4.5 to 4.5.4 and gpu-gromacs-beta 1, 2 versions. But it still doesn't work. any idea on thi