Re: [gmx-users] help required in calculating npme value for domain decomposition

Please refer to documentation on tune_pme in version 5.1.2 or g_tune_pme in older versions of gromacs. Regards, Sarath On 19 May 2016 at 23:43, Antara mazumdar wrote: > Dear gromacs users, > > I need help in calculating the value of npme for the purpose of domain >

Re: [gmx-users] simulation_time[Nikita Bora]

Thanks Tsjerk That was really a good explanation. And it helped me out a lot. Still,I would like to know what are the standard values for these parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used. As earlier it was mentioned that with different force field different value is used so is

[gmx-users] help required in calculating npme value for domain decomposition

Dear gromacs users, I need help in calculating the value of npme for the purpose of domain decomposition for my system of mixed lipid vesicles. Thanks!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

Dear users, Is there any script available to calculate % occupancy of residues with respect to time? This in continuation with my previous query on percentage of protein in contact with membrane?? Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of

Re: [gmx-users] Pull code slows down mdrun -- is this expected?

Dear Szilárd: I think that my ranks were set up similarly for GPU and non-GPU runs, though you can see how I ran the jobs below. One thing that I also already checked, but that I have not pasted here, is that all runs got the same DD and PME grid reported from the log file (4x1x1 for each in

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

Hi Antara, You can also simply calculate the ratio of buried surface area to total surface area, which you can both get with gmx sasa Cheers, Tsjerk On Thu, May 19, 2016 at 3:10 PM, Sarath Chandra < sarathchandrada...@gmail.com> wrote: > You can use g_contacts tool which will give you list of

Re: [gmx-users] Parameterization of OPLS-AA force field for MoS2 simulation in GROMACS.

Hi Barret, authors of that paper state which units they are using for energy, distance and angles - all other units might be inferred from units reasoning. For your specific concern, kb must have units of eV/Ų in their tables of parameters, leading to kJ/mol/nm² in the GROMACS convention after

Re: [gmx-users] Generating topology for a hem protein

On 5/19/16 9:41 AM, zeineb SI CHAIB wrote: Dear all, I'm desperetly looking for help to generate the topology of my hem protein. I'm using CHARMM as a force field and apparently PDB2gmx assigns dihedrals that should not exist and it's complicated to verify everything. Justin suggested

[gmx-users] Generating topology for a hem protein

Dear all, I'm desperetly looking for help to generate the topology of my hem protein. I'm using CHARMM as a force field and apparently PDB2gmx assigns dihedrals that should not exist and it's complicated to verify everything. Justin suggested using

Re: [gmx-users] Help required for calculation of protein coverage % wrt time

You can use g_contacts tool which will give you list of residues which are in contact with the membrane and their frequencies. You might have to write an overhead script to convert the residues in contact to %Protein in contact http://www.sciencedirect.com/science/article/pii/S0010465513002464

[gmx-users] Help required for calculation of protein coverage % wrt time

Dear gromacs users, I have a peripheral membrane protein which I have simulated using Charmm 36 in a mixed lipids bilayer. I want to calculate the percentage of protein in contact with membrane wrt time. I already have residue wise distances from membrane calculated. Can anyone suggest me how to

Re: [gmx-users] Gromacs installation.

http://gerrit.gromacs.org/download/regressiontests-5.0.4.tar.gz I think that something makes this link not downloadable. When I disable the download from -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON by deleting -DREGRESSIONTEST_DOWNLOAD=ON asking me to make GMX_BUILD_UNITTESTS=ON Then