[gmx-users] pull code with defined negative relative displacements
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Sun Nov 15 17:31:06 CET 2009
Hi Berk, I am aware that pull_init=4.75 should pull to 4.75, not 1.0.
I was mixing results from my simulations as I was discussing, sorry.
Please allow me to restate the issue: If I am indeed pulling to 4.75
below group 0, then why is the force positive when group 1 has a
displacement of -4.68988 (see below):
coord.xvg:
1669.4000 4.97979 -4.68988
force.xvg:
1669.4000 30.0622
I think that pull_geometry=distance and pull_geometry=direction are
not going to work here.
I have moved to a test system that is the a box of water in which I
pull the z of one water to a relative displacement with respect to one
other water.
From this, I have found that pull_geometry=position while passing in
a negative pull_init1 and a pull_vec1 of 0 0 0, appears to be the only
way to get this done.
Thank you for all of your time,
Chris.
> 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.
>> >
>> >
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
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> Message: 3
> Date: Sun, 15 Nov 2009 12:33:55 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] pull code with defined negative relative
> displacements
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W64796A20596537D4FB68AE8EA60 at phx.gbl>
> 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: 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.
>> >
>> >
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.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
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