Re: [gmx-users] Doubt in Gromacs nsteps, ps and ns

Hi Salam, Please get acquainted with SI units and prefixes. And don't forget to use your brains. It says there that 1000 ps is 1 ns. So now, how to go from 1 to 10 and match the ps and nsteps? Cheers, Tsjerk On Jan 30, 2015 8:55 AM, "salam pradeep" wrote: > Dear Gromacs user, > > I am a new us

[gmx-users] How to compute persistence length in gromacs

Hi all, I used g_polystat command in gromacs to compute persistence length and I define atom group in index.ndx file. The result is like Average end to end distance: 0.203 (nm) Average radius of gyration: 0.051 (nm) Average persistence length: *2.00 bonds* (? why not in nm?) Regards, -- Gr

Re: [gmx-users] Doubt in Gromacs nsteps, ps and ns

Thx a lot Tsjerk On Fri, Jan 30, 2015 at 1:38 PM, Tsjerk Wassenaar wrote: > Hi Salam, > > Please get acquainted with SI units and prefixes. And don't forget to use > your brains. It says there that 1000 ps is 1 ns. So now, how to go from 1 > to 10 and match the ps and nsteps? > > Cheers, > > Tsj

Re: [gmx-users] How to compute persistence length in gromacs

On 1/30/15 3:10 AM, Christian Bope Domilongo wrote: Hi all, I used g_polystat command in gromacs to compute persistence length and I define atom group in index.ndx file. The result is like Average end to end distance: 0.203 (nm) Average radius of gyration: 0.051 (nm) Average persistence

Re: [gmx-users] Energy minimization for Inositol pyrophosphate

On 1/30/15 1:55 AM, ashish bihani wrote: Hello, I understand that .itp is a topology file. But the swissparam pack does not have a .gro file. How do I create solvated.gro ? (which has to be used in grompp) Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say wheth

Re: [gmx-users] How to compute persistence length in gromacs

Thank you justin for reply. I have read and follow the second paragraph and use this command *g_polystat -s tmp.tpr -f tmp.xtc -n index.ndx -p persist.xvg* On 30 January 2015 at 19:14, Justin Lemkul wrote: > > > On 1/30/15 3:10 AM, Christian Bope Domilongo wrote: > >> Hi all, >> >> I used

Re: [gmx-users] Importing a trajectory into MOE

Hi Adam I have a SVL script to convert a gromacs trajectory in pdb format to mdb. Contact me offline. Best Sandeep On Wed, Jan 28, 2015 at 5:43 AM, adam wrote: > Hi > > > > Does anyone have experience/tips/ideas about importing a Gromacs trajectory > into MOE ? I can obviously port everyth

[gmx-users] Covalent bond/crosslink formation with calcium

Dear Gromacs users, We are simulating a large nanofiber assembly composed of repeating units of peptides, and we have been trying to see how the addition of calcium would affect its behavior. We have already tried adding calcium ions in a random distribution, which we successfully did. But we a

[gmx-users] Segmentation fault in g_sas with bigger probe

Dear Gromacs users, I'm trying to see the part of a protein that are accessible to an average size antibody and to do that I'm calculating the Solvent Accessible Surface Area using a bigger probe (-probe 1.5 ). The problem is that every time (and with different machines) I have "Segmentation fault

[gmx-users] Segmentation fault in g_sas with bigger probe

Dear Gromacs users, I'm trying to see the part of a protein that are accessible to an average size antibody and to do that I'm calculating the Solvent Accessible Surface Area using a bigger probe (-probe 1.5 ). The problem is that every time (and with different machines) I have "Segmentation fault