[gmx-users] pull code with defined negative relative displacements
Berk Hess
gmx3 at hotmail.com
Sun Nov 15 12:10:28 CET 2009
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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