[GMX-USERS] Pull Code

[David L. Bostick]

Hi Justin,

That would be great!  Could you answer a question or two about things as
well?  I guess my concern is more about knowing what is going on when I use
the pull code.  I know what parameters I input for umbrella sampling, but
how do you validate that the restraint potential is working?.. Is there
some output besides the .pdo file?  I tried -debug for mdrun, but that was
cryptic.  Does the direction set of values also influence which components
of direction are restrained between group_1 and reference_group?.. For
example does direction = 0.0 0.0 0.1 mean that the spring acts only in the
z dimension?  .. or is that only the case for afm pulling or the direction
of position scaling for starting structure generation?

Since I couldn't determine whether umbrella sampling was working, I tried
using afm pulling with pullrate = 0.0 , which should be the same thing as
doing one run with umbrella sampling.  I checked the output forces with a
manually calculated force using my input spring constant and center of mass
data from g_traj, but the forces didn't jive.

Thanks in advance for any help you can offer,
David

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	
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On Thu, 28 Feb 2002, Justin MacCallum wrote:

> 
> 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 
> > 
> 
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