Re: [gmx-users] Bootstrapping using g_wham

Hi, sorry for this late comment, I just stepped over this thread. Bootstrapping is indeed slow, because a complete WHAM analysis must be done for each bootstrap. I usually do much less bootstraps (around 50 to 100 gives a reasonable estimate), less bins, and I sometimes I reduce the tolerance

Re: [gmx-users] Bootstrapping using g_wham

Hey, Most statistics texts on bootstrapping will advise taking in the order of a thousand bootstrap samples. Don't know about the number of bins, but in any case, the problem shouldn't be that hard computationally. Have you checked the process? Is it really still running, has it stalled? And how l

Re: [gmx-users] Bootstrapping using g_wham

On 6/14/12 5:51 PM, rainy908 wrote: Hi, I am currently using bootstrapping in g_wham to estimate the uncertainty in my PMF. I use a number of 1000 bootstraps. /software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \ -ip gwham.dat \ -bins 5000 \ -hist histo.xvg \ -bsres bsRe

[gmx-users] Bootstrapping using g_wham

Hi, I am currently using bootstrapping in g_wham to estimate the uncertainty in my PMF. I use a number of 1000 bootstraps. /software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \ -ip gwham.dat \ -bins 5000 \ -hist histo.xvg \ -bsres bsResult.xvg \ -nBootstrap 1000 This process