Re: [gmx-users] pmf_calculation

2011-08-11 Thread Justin A. Lemkul
shahid nayeem wrote: Both files hist.xvg and profile.xvg both are simultaneous output of this command. I did not run it twice, once to get profile.xvg and then to get hist.xvg as you uderstood. They cannot be simultaneous output. The file named "hist.xvg" contains a PMF profile and has a

Re: [gmx-users] pmf_calculation

2011-08-11 Thread shahid nayeem
Both files hist.xvg and profile.xvg both are simultaneous output of this command. I did not run it twice, once to get profile.xvg and then to get hist.xvg as you uderstood. On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul wrote: > > > shahid nayeem wrote: > >> I used following command >> g_wham

Re: [gmx-users] pmf_calculation

2011-08-11 Thread Justin A. Lemkul
shahid nayeem wrote: I used following command g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files. An identical command with identical input files producing totally different o

Re: [gmx-users] pmf_calculation

2011-08-11 Thread shahid nayeem
I used following command g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files. shahid Nayeem On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul wrote: > > > shahid nayeem wrote: > >>

Re: [gmx-users] pmf_calculation

2011-08-11 Thread Justin A. Lemkul
shahid nayeem wrote: Dear Justin I did some more sampling and sending you profile.xvg, histo.xvg. and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell my the difference in profile.xvg and hist.xvg. Both should be same but I get different curves here. I can't tell yo

Re: [gmx-users] pmf_calculation

2011-07-05 Thread Justin A. Lemkul
shahid nayeem wrote: Dear Justin Here is my histogram file which does not show any window overlap. The sampling window I choose was 0.2 nm which I think is very large. Please suggest. The attached file contains a PMF profile, not histograms. That's in histo.xvg; not what you're calling "h

[gmx-users] pmf_calculation

2011-07-05 Thread shahid nayeem
Dear Justin Here is my histogram file which does not show any window overlap. The sampling window I choose was 0.2 nm which I think is very large. Please suggest. Shahid nayeem hist.xvg Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/l

Re: [gmx-users] pmf_calculation

2011-07-05 Thread Justin A. Lemkul
shahid nayeem wrote: Please the histogram generated. It does not show any window overlap. You have some regions where the overlap is good, some where it is weak, and some where it is nonexistent. You either need more sampling or more windows to capture the entire reaction coordinate. This

Re: [gmx-users] pmf_calculation

2011-07-05 Thread Justin A. Lemkul
shahid nayeem wrote: Dear Justin I did pmf calculation for my protein-protein complex using your tutorial.Off course changing the pull_direction suitable for my protein but more or less following the same strategy. I am using gromacs_4.5.4 and g_wham utility. The profile.xvg file which I get

[gmx-users] pmf_calculation

2011-07-05 Thread shahid nayeem
Dear Justin I did pmf calculation for my protein-protein complex using your tutorial.Off course changing the pull_direction suitable for my protein but more or less following the same strategy. I am using gromacs_4.5.4 and g_wham utility. The profile.xvg file which I get is attached and it shows tw