Re: [gmx-users] g_wham error analysis hangs

Hi Jochen, Seems as if this error was associated with the mpi version. Everything worked ok when running it locally. Best regards / Magnus On Aug 12, 2013, at 1:50 PM, Jochen Hub wrote: > Hi Magnus, > > I just read your mail. Sound very much like a bug, which never occurred > to me though.

Re: [gmx-users] g_wham error analysis hangs

Hi Magnus, I just read your mail. Sound very much like a bug, which never occurred to me though. But I did not use -bs-method traj-gauss a lot. Does the error also occur with -bs-method traj? Btw: with -bs-method traj-gauss or traj, you need realistic estimates of the autocorrelation times (ACTs)

Re: [gmx-users] g_wham error analysis hangs

On 8/5/13 8:21 AM, Magnus Andersson wrote: What version of Gromacs are you using? How many data points do you have in the full set? -Justin Gromacs 4.6 not sure what you mean by data points, but: dt = 0.002 nsteps = 100 Not relevant, but

Re: [gmx-users] g_wham error analysis hangs

> What version of Gromacs are you using? How many data points do you have in > the full set? > > -Justin > Gromacs 4.6 not sure what you mean by data points, but: dt = 0.002 nsteps = 100 and total number of atoms in the system: 265,891 # frames

Re: [gmx-users] g_wham error analysis hangs

On 8/5/13 8:06 AM, Magnus Andersson wrote: I've had this happen before when trying to analyze too many data points. Try reducing the size of the input data using -b to see if that helps. -Justin Thanks for the suggestion, Justin. However, either it hangs or I get: Fatal error: Tryig to

Re: [gmx-users] g_wham error analysis hangs

> > I've had this happen before when trying to analyze too many data points. Try > reducing the size of the input data using -b to see if that helps. > > -Justin Thanks for the suggestion, Justin. However, either it hangs or I get: Fatal error: Tryig to estimtate autocorrelation time from on

Re: [gmx-users] g_wham error analysis hangs

On 8/5/13 2:29 AM, Magnus Andersson wrote: Hi, I have a problem with the error analysis of g_wham. The PMF profile and sampling windows looks good, but when I try to generate error bars g_wham hangs. This is what I do: g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 5

Re: [gmx-users] g_wham error

rajat desikan wrote: Sorry, sorry...I have used Opls AA. The methane was going back and forth in the pulling during which I generated the configurations. Assuming you used a harmonic potential, that is to be expected. As long as you have set up reasonable spacing for your sampling windows

Re: [gmx-users] g_wham error

rajat desikan wrote: Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple This is fundamentally incorrect. 53A6 is a united-atom force field, so each methane should be a single particle with 0 charge usi

Re: [gmx-users] g_wham error

Yeah, I have partial charges on, -0.24 on carbon and + 0.06 on the hydrogens...I am using Gromos 96 53a6 force field. I am getting a couple of doubts Justin. Since, I am pulling the methane away steadily, it should smoothly increase the distance right? But the second methane molecule is both increa

Re: [gmx-users] g_wham error

rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model of methane, you should have partial charges. -Justin On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul

Re: [gmx-users] g_wham error

Justin, Should i turn off charges on the methane molecules? I have left them on. On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul wrote: > > > rajat desikan wrote: > >> My simulations are for 10 ns in each window. There is a lot of noise in >> my wham too. I am enclosing my wham for pullf (the

Re: [gmx-users] g_wham error

rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham for pullf (the earlier was pullx) and pmf. They are really looking strange. Stronger restraint means force constant? >From literature, I kept it at 3000. Those

Re: [gmx-users] g_wham error

rajat desikan wrote: hi Justin I am not able to tell where the lack of overlap is. This is the first wham plot I am looking at. In your tutorial and literature, the wham plots are so clear. Can you please help me? Thanks. It looks like your first one or two windows were not restrained suf

Re: [gmx-users] g_wham error

Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul wrote: > > > rajat desikan wrote: > >> Hi >> I am a new gromacs user. I just completed Justin's umbrella sampling >> tutorial. I am doing a PMF calculation between 2 methane molecules in >> wat

Re: [gmx-users] g_wham error

rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules in water. The simulation has run fine till the g_wham step. My command is -- g_wham -it tpr-files.dat -if pullf-files.dat -o -hist

Re: [gmx-users] g_wham error

g_wham -ix PREPxvg.dat -it PREPtpr.dat The -ix option expects the pull positions. If you want to provide the pull forces to g_wham, use the -if option. Cheers, Jochen PREPxvg.dat and PREPtpr.dat are lists of the respective xvg and tpr files. They are both in the same order, although

Re: [gmx-users] g_wham error

Justin A. Lemkul wrote: Gard Nelson wrote: Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 Note, too, that this command doe

Re: [gmx-users] g_wham error

Gard Nelson wrote: Here's my .xvg: # This file was created Mon Mar 8 01:50:07 2010 # by the following command: # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdrun_mpi -multi 31 -deffnm onePREP -px onePREP -np 2976 -maxh 3 # # /opt/apps/intel10_1/mvapich1_1_0_1/gromacs/4.0.5/bin/mdr

Re: [gmx-users] g_wham error

Gard Nelson wrote: Hi all, I'm trying to analyze a series of umbrella sampling windows, but I get the following error: Program g_wham, VERSION 4.0.7 Source code file: gmx_wham.c, line: 1397 Fatal error: Found 1 pull groups in onePREP0.tpr, but 1 data columns in onePREP0.xvg (expected 6) m

Re: [gmx-users] g_wham error

Ragnarok sdf wrote: While trying to analyse my several windows with g_wham the following error appears : Fatal error: Pull geometry direction not supported The pull geometry "direction" has unfortunatly been forgotten in g_wham by, well, myself (shame on me :-) ). I can add the geometry to

Re: Re: [gmx-users] g_wham error

> > > > > Ragnarok sdf wrote: > > > While trying to analyse my several windows with g_wham the > > following error > > > appears : > > > > > > Fatal error: > > > Pull geometry direction not supported > > > > > > my entry files consist on the several px.xvg

Re: [gmx-users] g_wham error

> > > > Ragnarok sdf wrote: > > > > Ragnarok sdf wrote: > > > While trying to analyse my several windows with g_wham the > > following error > > > appears : > > > > > > Fatal error: > > > Pull geometry direction not supported > > > > > > my entry files con

Re: [gmx-users] g_wham error

Ragnarok sdf wrote: Ragnarok sdf wrote: > While trying to analyse my several windows with g_wham the following error > appears : > > Fatal error: > Pull geometry direction not supported > > my entry files consist on the several px.xvg listed in a .dat

Re: [gmx-users] g_wham error

Ragnarok sdf wrote: While trying to analyse my several windows with g_wham the following error appears : Fatal error: Pull geometry direction not supported my entry files consist on the several px.xvg listed in a .dat entry file and the several .tpr from each of the simulations also listed in

Re: [gmx-users] g_wham error

mirc...@sjtu.edu.cn wrote: > gunzip: stdin: not in gzip format > > --- > Program g_wham, VERSION 3.3.3 > Source code file: gmx_wham.c, line: 89 > > Fatal error: > This does not appear to be a valid pdo file > ---

Re: [gmx-users] g_wham Error bars

Raphael Alhadeff wrote: > Hello everyone, > > I wanted to ask if anyone knows how to compute standard deviation, for the > sake of adding error bars to an energy profile output using g_wham (PMF using > umbrella sampling in my case). > > Just to clarify, I am talking about the deviation of the

Re: [gmx-users] g_wham Error bars

Hello, As far as I know, it is not possible to directly calculate and error bar with g_wham . At that point, you've got several options: 1) You can run several times your umbrella sampling simulations, calculate several PMFs, then calculate an average and a standard deviation 2) i