[gmx-users] analysis of PMF calculations

[Justin A. Lemkul]

Rebeca García Fandiño wrote:
> Hi,
> thanks a lot for your quick answer...
> However, when I try the options you suggest for -cycl/nocycl, the 
> program indeed ask for arguments:
> 
> -------------------------------------------------------
> Program g_wham, VERSION 4.5
> Source code file: statutil.c, line: 338
> 
> Fatal error:
> Expected a string argument for option -cycl
> -----------------------------------------------------------------
> 

Upgrade to version 4.5.4 and try again.  There have been improvements to g_wham.

> Besides, I think you have misunderstood me. When I use the option -cycl 
> YES it's when I obtain the second column with zeros. I am working with a 

Based on what your message said, I thought I understood perfectly.  Quoting:

---
When I use:

/GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max 
2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip ./pdo-files.dat -cycl yes

I get a curve with no errors, however if I don't use the option "-cycl yes"
---

Here everything sounds like it worked as expected and then you report the error, 
quoting again:

---
/GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 -max 
2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg -ip ./pdo-files.dat

I get a profile where the second column is all "zero"
---

Nevertheless, you should still use version 4.5.4 g_wham and report back if you 
have problems.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================