[gmx-users] Pull Code problems
Berk Hess
gmx3 at hotmail.com
Tue Jan 13 16:32:32 CET 2009
Hi,
pullx.xvg has the coordinates of group 0 and the distances
of the other groups to group 0.
pullf.xvg has the force of the umbrella potential
which works along the direction vector you gave,
this can be positive or negative depending on the direction.
Berk
> Subject: RE: [gmx-users] Pull Code problems
> From: genesup at gmail.com
> To: gmx-users at gromacs.org
> Date: Tue, 13 Jan 2009 18:02:47 +0300
>
> OK,
> I did some homework and now I`m up to this:
>
> ;-----------PULL CODE ---------------------
>
> pull = umbrella
> pull_geometry = direction
> pull_group0 = r_500
> pull_group1 = r_535
> pull_vec1 = -1.306 1.355 -0.319
> pull_k1 = 1000
> pull_rate1 = 0.5 ; nm/ps Extreme parameters for extreme pulling
>
> Now I have two output files - pullx.xvg (-px option of mdrun) and
> pullf.xvg (-pf option).
>
> pullx :
>
> @ title "Pull COM"
> @ xaxis label "Time (ps)"
> @ yaxis label "Position (nm)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "0 X"
> @ s1 legend "0 Y"
> @ s2 legend "0 Z"
> @ s3 legend "1 dX"
> @ s4 legend "1 dY"
> @ s5 legend "1 dZ"
> 0.000000 3.899593 5.816368 3.246447
> -0.285972 -0.132647 -0.183023
> 0.040000 3.901163 5.812132 3.238992
> -0.292108 -0.141616 -0.180796
> 0.080000 3.902505 5.806212 3.240236
> -0.314770 -0.143951 -0.186194
> 0.120000 3.905365 5.797938 3.242384
> -0.336802 -0.142276 -0.197704
> 0.160000 3.908899 5.794812 3.230687
> -0.342824 -0.160593 -0.178745
> 0.200000 3.910108 5.797564 3.220754
> -0.340151 -0.161146 -0.152076
>
> Am I correct about XYZ being position of the spring and dx dy dz -
> group0-group1 distances?
>
> pullf :
>
> @ title "Pull force"
> @ xaxis label "Time (ps)"
> @ yaxis label "Force (kJ/mol/nm)"
> @TYPE xy
> 0.000000 -132.088161
> 0.004000 -128.605515
> 0.008000 -125.008520
> 0.012000 -121.568624
> 0.016000 -118.475655
> 0.020000 -115.844403
> 0.024000 -113.735184
> 0.028000 -112.165522
> 0.032000 -111.066433
> ..... .......
> 1.232000 409.573773
> 1.236000 412.738957
> 1.240000 415.736038
> 1.244000 418.446270
> 1.248000 420.781766
> 1.252000 422.747570
> 1.256000 424.505472
> 1.260000 426.348269
> 1.264000 428.568933
> 1.268000 431.301610
> 1.272000 434.467394
>
> Why does it start with negative values? Should I use negative value for
> pull_k1 (force constant)?
>
> Thank you for your answers, I appreciate your time.
>
> SDA
>
>
>
> On Tue, 2009-01-13 at 12:41 +0100, Berk Hess wrote:
> > Hi,
> >
> > You don't indicate which xvg file was 0, I guess pullf.xvg.
> > Could it be that you did not specify a force constant, meaning fc=0?
> >
> > Berk
> >
> > > From: genesup at gmail.com
> > > To: gmx-users at gromacs.org
> > > Date: Tue, 13 Jan 2009 14:26:47 +0300
> > > Subject: [gmx-users] Pull Code problems
> > >
> > > Hello,
> > >
> > > I am trying to run a pulling simulation with gromacs 4.0.2.
> > >
> > > I have appended the following pull code to the mdp file:
> > >
> > > ;-----------PULL CODE ---------------------
> > >
> > > pull = umbrella
> > > pull_geometry = direction
> > > pull_group0 = r_500
> > > pull_group1 = r_535
> > > pull_vec1 = -1.306 1.355 -0.319
> > >
> > > Where r_500 is the group I am expecting to be pulled,
> > > r_535 - the reference (the acid that is in fact in contact with
> > > r_500)
> > >
> > > I have left all remaining parameters with default values.
> > >
> > > The problem is that NOTHING HAPPENED! XVG file had 0.0000 throughout
> > > simulation indicating that distance between pull group and reference
> > > group was 0!
> > >
> > > 1/ What did I do wrong?
> > > 2/ Is there any pull code tutorial for gromacs 4 (not previous
> > > version)?
> > >
> > > Thank you!
> > > SDA
> > >
> > > _______________________________________________
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