[gmx-users] Installation Error

Hi Justin, I am trying to install gromacs-4.5.5 on a Linux work station (x86_64) but I am getting an error. The error message is attached in the mail in a text file "Installation_error.txt". I have installed fftw-3.3.3 in my system. I have checked threads on the mailing list which have reporte

Re: [gmx-users] GROMACS 4.6-beta2 released

Speed-up depends what you measure against, what precision GROMACS is using, and what your AVX hardware is. There is no single number worth mentioning. GROMACS has different AVX kernels for single vs double, and Intel Sandy Bridge / Ivy Bridge vs AMD's Opteron / Bulldozer. I haven't seen any numbers

[gmx-users] Fwd: [gmx-developers] cmake bug when install GMX 4.6 beta2

Hi Yukun, In future, please only target email associated with GROMACS development to the gmx-developers mailing list. gmx-users is for usage questions, such as installation issues. I am replying to this email to both lists. If you've correctly installed and used icc 11.1, then I think you should

Re: [gmx-users] Installation Error

See http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite On Fri, Dec 7, 2012 at 9:08 AM, BHARATI DUTTA wrote: > > Hi Justin, > > I am trying to install gromacs-4.5.5 on a Linux work station (x86_64) but > I am getting an error. The error me

[gmx-users] Extending REMD simulations problem

Hi all, i want to extend a remd simulation that finished correctly, but i always get the same segmentation fault error. This is what i am doing with a test system. I run the REMD simulation with: mdrun_mpi_d -s test_.tpr -deffnm test_ -multi 2 -replex 500 After the simulation correctly finis

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Today I've tried to simulate complexes of my protein with the cyclic GMP parametrized by ATB's. (below the recent parametrisation for charges of that molecule done by am1 algorithm) [ moleculetype ] ; Name nrexcl _N4P 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 12/7/12 10:41 AM, James Starlight wrote: Today I've tried to simulate complexes of my protein with the cyclic GMP parametrized by ATB's. (below the recent parametrisation for charges of that molecule done by am1 algorithm) [ moleculetype ] ; Name nrexcl _N4P 3 [ atoms ] ; nr type r

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Justin, ligand-only simulation in vacuum have been finished with the same errors :) Step 19200, time 38.4 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.025443, max 0.140660 (between atoms 1 and 3) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, cur

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 12/7/12 11:42 AM, James Starlight wrote: Justin, ligand-only simulation in vacuum have been finished with the same errors :) Step 19200, time 38.4 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.025443, max 0.140660 (between atoms 1 and 3) bonds that rotated more than

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Justin, following to your advise I've tried to use charmm 27 ff for simulation of my protein-cGMP complex ( ligand was parametrized by Swiss Param server). Could you provide me with the cut-offs for vdw as well as electrostatics suitable for simulation in charmm27 and 36 force fields? Does anybo

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 12/7/12 1:19 PM, James Starlight wrote: Justin, following to your advise I've tried to use charmm 27 ff for simulation of my protein-cGMP complex ( ligand was parametrized by Swiss Param server). Could you provide me with the cut-offs for vdw as well as electrostatics suitable for simulati

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

Justin, with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp NOTE 1 [file ./mdps/em.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. NOTE 2 [fil

Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

On 12/7/12 2:21 PM, James Starlight wrote: Justin, with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp NOTE 1 [file ./mdps/em.mdp]: For energy conservation with switch/shift potentials, rlist should b

[gmx-users] Specifying no temperature coupling in contrast to grompp output

Hi, In my .mdp file, I set "tcoupl = no" and "pcoupl = no". This way, I am using the NVE ensemble. However, when I run grompp using this .mdp file, the grompp output includes the following line: Number of degrees of freedom in T-Coupling group rest is 261.00 My question is, why does the grompp

Re: [gmx-users] Specifying no temperature coupling in contrast to grompp output

On 12/7/12 4:06 PM, Andrew DeYoung wrote: Hi, In my .mdp file, I set "tcoupl = no" and "pcoupl = no". This way, I am using the NVE ensemble. However, when I run grompp using this .mdp file, the grompp output includes the following line: Number of degrees of freedom in T-Coupling group rest

Re: [gmx-users] area per lipid

Hi again, I edited my md.mdp files. I'm wondering if my nvt.mdp and npt.mdp in charmm36 ff also need such a edition? Also I'd like to know if these mdp file are applicable in any simulation done with charmm36? Sincerely, Shima From: Justin Lemkul To: Shima