[gmx-users] g_wham error

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 16 22:13:35 CET 2010

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 doesn't make much sense.  By using -deffnm, you 
specify the default input and output file names.  Using -px with the same name 
has no purpose.  Did your files write over each other?  I've never done things 
this way, I will usually specify -deffnm, but in conjunction with something like:

mdrun -deffnm md -pf pullf_md -px pullx_md

That way, there's no ambiguity.  Trajectories, etc. are written to md.* and the 
output pertinent to the pull code is saved in pullf_md.xvg and pullx_md.xvg.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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