[gmx-users] Pull Code problems

[DimitryASuplatov]

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
> > 
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> ______________________________________________________________________
> What can you do with the new Windows Live? Find out