[gmx-users] pull code with defined negative relative displacements

Berk Hess gmx3 at hotmail.com
Sun Nov 15 12:33:55 CET 2009


Hi,

I only now noticed Justin mail on g_wham.
You can probably also use pull_geometry=distance and pull_init=1,
if you starting structure has group1 close to 1 nm below group 0.

Berk

From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] pull code with defined negative relative displacements
Date: Sun, 15 Nov 2009 12:10:28 +0100








Hi,

pull_init should be 1, not 4.75, if you want group1 to be 1 nm below group0.
Alternatively you can have vec = 0 0 1 and pull_init = -1.

Berk

> Date: Sat, 14 Nov 2009 14:54:54 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> 
> Hi Justin, (comment to Berk below)
> 
> thanks for pointing out the g_wham problem. I am personally ok here as  
> I use a non-gromacs wham program.
> 
> Hi Berk,
> 
> unless I misunderstood, your suggestion does not yield the gromacs 3  
> behaviour that I am trying to reproduce with gromacs 4.
> 
> If I simply misunderstood your suggestion, can you please be a little  
> more explicit? What I want to do is to harmonically restrain the COM  
> of group 1 to be X nm more negative along Z than the COM of group 0.  
> It is important that this still works when the value for X is smaller  
> than the standard deviation of the sampled values such that the  
> distribution does not become bimodal.
> 
> Here is the test using pull_geometry=direction, and I note that this  
> is exactly the same behaviour that I observed and posted in my last  
> email while using pull_geometry=distance in combination with pull_vec.
> 
> pull                     = umbrella
> pull_geometry            = direction
> pull_dim                 = N N Y
> pull_start               = no
> pull_nstxout             = 10
> pull_nstfout             = 10
> pull_ngroups             = 1
> pull_group0              = POPC
> pull_pbcatom0            = 0
> pull_group1              = Protein
> pull_pbcatom1            = 0
> pull_init1               = 4.75
> pull_rate1               = 0
> pull_k1                  = 500.0
> pull_vec1               = 0 0 -1
> 
> 
> coord.xvg:
> 1669.4000       4.97979 -4.68988
> force.xvg:
> 1669.4000       30.0622
> Where the force should be -30.062 (assuming that I understand  
> everything correctly).
> 
> coord.xvg:
> 2.9600  5.16151 -5.14321
> force.xvg
> 2.9600  -196.603
> Where the force should be +196.603 (assuming that I understand  
> everything correctly).
> 
> pull                     = umbrella
> pull_geometry            = direction
> pull_dim                 = N N Y
> pull_start               = no
> pull_nstxout             = 10
> pull_nstfout             = 10
> pull_ngroups             = 1
> pull_group0              = POPC
> pull_pbcatom0            = 0
> pull_group1              = Protein
> pull_pbcatom1            = 0
> pull_init1               = 4.75
> pull_rate1               = 0
> pull_k1                  = 500.0
> pull_vec1               = 0 0 1
> 
> coord.xvg:
> 0.5200  5.17421 5.00621
> force.xvg:
> 0.5200  -128.107
> Where this is what I intend to occur (i.e. working as I desire it to).
> 
> coord.xvg:
> 1649.4000       4.99895 4.69239
> force.xvg:
> 1649.4000       28.807
> Where this is what I intend to occur (i.e. working as I desire it to).
> 
> 
> 
> 
> Thank you,
> Chris.
> 
> --- original message --
> 
> Hi,
> 
> You should use pull_geometry=direction.
> distances don't get negative.
> 
> Berk
> 
> > Date: Sat, 14 Nov 2009 09:21:39 -0500
> > From: chris.neale at utoronto.ca
> > To: gmx-users at gromacs.org
> > Subject: [gmx-users] pull code with defined negative relative displacements
> >
> > Hello, I am re-running some of our gromacs 3 simulations using gromacs
> > 4, and as far as I can tell the gromacs 4 pull code, while very nicely
> > enhanced from gromacs 3, has also lost some functionality.
> >
> > I am calculating the PMF of a peptide across a bilayer and, to   
> > simplify the issue, what I can't figure out how to do with gromacs 4  
> >  is to pull group1 to a position 1 nm more negative along the z-axis  
> >  than group 0 (the bilayer in this case) for some replicas and to 1  
> > nm  more positive along the z-axis than group 0 in others. I'll  
> > focus on  the negative displacement here as it is the one that is  
> > giving me  problems.
> >
> > This used to be possible with the following gromacs 3 pull.ppa options:
> >
> > runtype   = umbrella
> > reftype   = com
> > pulldim   = N N Y
> > reference_group = group0
> > group_1   = group1
> > K1        = 500
> > Pos1      = 0 0 -1.0
> >
> > Sure, I could start group1 in the correct negative-z displacement from
> > group0 and use pull_init1=+1.0, but this will not work when, for
> > instance, I want to restrain it to -0.1 nm (using pull_init1=+0.1),
> > where the sampling will infrequently jump back and forth about z=0.
> >
> > Just to be sure, I tried for gromacs 4 are the following pull code   
> > .mdp options:
> >
> > pull                     = umbrella
> > pull_geometry            = distance
> > pull_dim                 = N N Y
> > pull_start               = no
> > pull_ngroups             = 1
> > pull_group0              = group0
> > pull_group1              = group1
> > pull_init1               = -1.0
> > pull_rate1               = 0
> > pull_k1                  = 500.0
> >
> > where mdrun complains:
> > "Pull reference distance for group 1 is negative (-1.000000)"
> >
> > and it is pretty obvious why this doesn't work since it is asking for
> > a negative displacement. Nevertheless, I tried it and pull_init1
> > appears to get set to zero.
> >
> > I also attempted the following.
> >
> > pull                     = umbrella
> > pull_geometry            = distance
> > pull_dim                 = N N Y
> > pull_start               = no
> > pull_ngroups             = 1
> > pull_group0              = group0
> > pull_group1              = group1
> > pull_init1               = 1.0
> > pull_rate1               = 0
> > pull_k1                  = 500.0
> > pull_vec1                = 0 0 -1
> >
> > where I would then use
> > pull_init1 = 1.0
> > pull_vec1  = 0 0 1
> > for the positive side of the bilayer.
> >
> > However, when I look at the forces, I am getting the negative of  
> > what  I should get when pull_vec1 = 0 0 -1.
> >
> > coord.xvg:
> > 610.0000	4.9343	-1.02019
> > 660.0001	4.91454	-0.949747
> >
> > force.xvg:
> > 610.0000	-10.0932
> > 660.0001	25.1265
> >
> > Although I am getting exactly what I should get when pull_vec1 = 0 0  
> > 1  (for intended positive displacements).
> >
> > coord.xvg:
> > 660.0001	4.9014	1.16304
> >
> > force.xvg:
> > 660.0001	-81.5201
> >
> > Any ideas are greatly appreciated. I can probably mod the code for my
> > needs, but a standard gromacs binary is always preferable.
> >
> > Thank you,
> > Chris.
> >
> >
> 
> 
> -- 
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