[GMX-USERS] Pull Code

[Justin MacCallum]

Hi David,

I'm not sure what the status of the pull code in the released version of
Gromacs is.  Here in Calgary we have a locally  modified version that I
have been using for some time that has correctly working umbrella
sampling.  I'm currently working on adding a few more features and getting
the whole thing into the CVS tree so it will become part of the
distribution, but I'm kind of swamped at the momement so it may take a
while.

If you're interested, I can send you a copy of the current working code.
If you email me at jlmaccal at ucalgary.ca, I will send you a copy of the
code and some details on a calculation I did for the PMF of hexane across
a bilayer.

Justin

> Hello all,
> 
> I want to measure the pmf of an ion traversion across a membrane protein.
> I haven't decided whether I want to use umbrella sampling or constraint
> force measurement but I'm playing with the pull code for both.  However, I
> want to constrain/restrain (constraint force sampling / umbrella sampling)
> the ion with respect to the protein backbone in the z dimension only.  Is
> this possible with the input.ppa options?  Does setting 
> 
> direction = 0.0 0.0 1.0 
> 
> do this?
> 
> So far, I have tried to measure constraint force with the following options
> in the .ppa file:
> 
> verbose                  = no
> runtype                  = constraint
> group_1                  = CL
> reference_group          = Backbone
> reftype                  = com
> reflag                   = 1
> direction                = 0.0 0.0 1.0
> 
> but I get Not a Number for my output forces.
> 
> I have also tried umbrella sampling for one point using:
> 
> verbose                  = no
> runtype                  = umbrella
> group_1                  = CL
> reference_group          = Backbone
> reftype                  = com
> reflag                   = 1
> direction                = 0.0 0.0 1.0
> width                    = 1000.0
> 
> but I get an output file with one set of 3D coordinates (of the group_1 I
> suppose) and another set of coordinates on the right side of the file ..
> all reading 0.0 0.0 0.0.
> 
> Can anyone offer any help?
> 
> David 
>