[gmx-users] problems with g_wham

凌未风 grx1985 at qq.com
Sun Mar 29 01:49:22 CET 2015


Hello, 

I have a very strange problem when using g_wham to generate PMF profiles, 

The command I am using is :
g_wham -if pullflist.dat -it tprlist.dat -o profiles.xvg -hist histo.xvg -min 0.5 -max 4.1 -bins 150 -temp 310 -zprof0 4.1 -b 2500000 -e 3000000

and I get the following errors:

WARNING, no data points read from file ./pullf/us4-devide.xvg (check -b option)
Reading file ./us3.9/us3.9.tpr, VERSION 4.6.5 (single precision)
WARNING, no data points read from file ./pullf/us3.9-devide.xvg (check -b option)
........

I checked my pullflist.dat as well as us4-devide.xvg and I am pretty sure that there are data in the files (there are no gaps in the data). 
When I using the following command:
g_wham -if pullflist.dat -it tprlist.dat -o profiles.xvg -hist histo.xvg  -min 0.5 -max 4.1 -bins 150 -temp 310 -zprof0 4.1 -b 500000 -e 1500000

Then it could give me PMF profile properly. The only difference is the parameters of -b and -e. 

I checked several times and I am 100% sure there are enough data in my files (from 0 ps to 3500000 ps) and the problem is that g_wham is not reading  the data, although the data are there.  I checked my data very carefully, and there are no gaps in my data, everything is fine. 
Why g_wham behave different when I assign different -b and -e values, since I am SURE I have data at each time frame? Why it is reading the data sometimes, but is not reading with different start and end points?

Does anyone have similar problems? Could anyone give some clue of how to solve this annoying problem?

With my best regards, 
RXG


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