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: [email protected]
To: [email protected]
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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Message: 3
Date: Sun, 15 Nov 2009 12:33:55 +0100
From: Berk Hess <[email protected]>
Subject: RE: [gmx-users] pull code with defined negative relative
displacements
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
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: [email protected]
To: [email protected]
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: [email protected]
To: [email protected]
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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