Re: [gmx-users] need tip3p.gro for charmm force field

On 19/06/2011 12:26 PM, sreelakshmi ramesh wrote: Dear all, am trying to do a simulation with charmm forcefield adn tip3p water model when i use gen box command adn mention tip3p gromacs gives a error that the tip3p file is not found.any help please regrds, sree See http://www.gromacs.or

[gmx-users] need tip3p.gro for charmm force field

Dear all, am trying to do a simulation with charmm forcefield adn tip3p water model when i use gen box command adn mention tip3p gromacs gives a error that the tip3p file is not found.any help please regrds, sree -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

Re: [gmx-users] is lincs used with virtual hydrogens?

On 19/06/2011 6:56 AM, Roland Schulz wrote: My understanding is that the v-site algorithm is used for the virtual sites and LINCS is used for bonds not involving v-sites (and also angles if you choose contraint=angles). Yep. Also, with the LINCS warning about over-rotation, I get that regular

Re: [gmx-users] is lincs used with virtual hydrogens?

On 19/06/2011 6:13 AM, chris.ne...@utoronto.ca wrote: Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? Sure - all the backbone bonds, for starters. I believe that it is, as if I use a t

Re: [gmx-users] standard deviation about rmsd and rmsf values

Hey, The rmsf and rmsd are themselves sort of standard deviations. They are chi distributed, and the confidence intervals are generally not characterized by a standard deviation, which would be a standard deviation of a standard deviation :p Cheers, Tsjerk On Jun 18, 2011 1:21 PM, "Francesco Ot

Re: [gmx-users] is lincs used with virtual hydrogens?

My understanding is that the v-site algorithm is used for the virtual sites and LINCS is used for bonds not involving v-sites (and also angles if you choose contraint=angles). On Sat, Jun 18, 2011 at 4:40 PM, chris.ne...@utoronto.ca < chris.ne...@utoronto.ca> wrote: > Thank you Roland. > > I did

[gmx-users] is lincs used with virtual hydrogens?

Thank you Roland. I did use: constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs From looking at the manual, I figured that angle and bond constraints would all be done by LINCS if I had done (A): pdb2gmx -vsite none constraints = h-angles (a combination t

Re: [gmx-users] is lincs used with virtual hydrogens?

On Sat, Jun 18, 2011 at 4:13 PM, chris.ne...@utoronto.ca < chris.ne...@utoronto.ca> wrote: > Dear Users: > > If I create the topology of a peptide like this: > > pdb2gmx -f protein.gro -vsite hydrogens > > And then simulate it in vacuum, is lincs used at all? I believe that > it is, as if I use a

[gmx-users] is lincs used with virtual hydrogens?

Dear Users: If I create the topology of a peptide like this: pdb2gmx -f protein.gro -vsite hydrogens And then simulate it in vacuum, is lincs used at all? I believe that it is, as if I use a timestep that is too large then I get LINCS warnings about angles rotating more than 30 degrees, but

Re: [gmx-users] standard deviation about rmsd and rmsf values

g_analyze -f file.xvg the program prints, for each data set, the average and standard deviation Il 18/06/2011 13:18, shahab shariati ha scritto: Dear gromacs users I want to know how to obtain standard deviation about rmsd and rmsf values? any help will highly appreciated. -- gmx-users ma

[gmx-users] standard deviation about rmsd and rmsf values

Dear gromacs users I want to know how to obtain standard deviation about rmsd and rmsf values? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mai