RE: [gmx-users] pull code with defined negative relative displacements
Hi, With only 1 pull dimension active (through pull_dims) all three geometries are equivalent. In 2 or 3D there are all different. With pull_geometry=direction the pull force is the force working along the direction vector. So in general you can't incorporate the direction (only sign in your case) into the force, unless you would print the whole vector. Berk > Date: Wed, 18 Nov 2009 12:12:49 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] pull code with defined negative relative displacements > > Hi Berk, > > I have done the tests and you are entirely correct. I have one further > question: If I simply want to pull to a relative displacement of -1.0 > nm, is there any reason to prefer one of these methods, or are they > just overlapping implementations of different methods that also have > unique abilities given other settings? > > To summarize my tests, pull_geometry=direction can indeed pull to negative > displacements and there is no bimodal behaviour. My misunderstanding > derived from the fact that > > pull_geometry= direction > pull_init1 = 1.0 > pull_vec1= 0 0 1 > > gave the forces as I expected them, while > > pull_vec1= 0 0 -1 > > reports the negative of the force that I expected. Since the force as > output is probably applied after multiplication by pull_vec1, it might > be more intuitive to simply output the force after it is multiplied by > pull_vec1 such that what is output is the actual applied force. But > then again there are probably some good reasons why it is output the > way that it is. > > I have included probability distribution plots for the sampling along z for > the tests below at: > http://i205.photobucket.com/albums/bb192/chrisneale_2007/X10.png (1.0 nm > displacement test) > http://i205.photobucket.com/albums/bb192/chrisneale_2007/X005.png (0.05 nm > displacement test) > http://i205.photobucket.com/albums/bb192/chrisneale_2007/X35.png (3.5 nm > displacement test) > > Thank you for all of your assistance, > Chris. > > # > Summary for attempts to pull to -1.0: > > ### Pulls to -1 > > pull_geometry= position > pull_init1 = 0 0 -1 > pull_vec1= 0 0 0 > > pull_geometry= direction > pull_init1 = -1.0 > pull_vec1= 0 0 1 > > pull_geometry= direction > pull_init1 = 1.0 > pull_vec1= 0 0 -1 > > ### Pulls to +1 > > pull_geometry= direction > pull_init1 = 1.0 > pull_vec1= 0 0 1 > > # > Detailed results: > > pull_geometry= position > pull_init1 = 0 0 -1 > pull_vec1= 0 0 0 > > $ tail coord.xvg > 98.2000 5.03064 -0.96114 > 98.4000 5.02906 -0.968864 > 98.6000 5.02755 -1.0196 > 98.8000 5.02577 -0.971355 > 99. 5.02408 -0.948518 > 99.2000 5.02289 -0.973627 > 99.4000 5.0227 -0.977471 > 99.6000 5.02293 -0.965711 > 99.8000 5.0242 -1.01475 > 100. 5.0251 -1.03216 > > $ tail force.xvg > 98.2000 -19.4299 > 98.4000 -15.568 > 98.6000 9.8014 > 98.8000 -14.3227 > 99. -25.741 > 99.2000 -13.1865 > 99.4000 -11.2644 > 99.6000 -17.1443 > 99.8000 7.37747 > 100. 16.0813 > > > > pull_geometry= direction > pull_init1 = 1.0 > pull_vec1= 0 0 1 > > $ tail coord.xvg > 98.2000 5.06691 1.09005 > 98.4000 5.06773 1.04829 > 98.6000 5.06842 1.02481 > 98.8000 5.06934 1.02874 > 99. 5.07061 0.995157 > 99.2000 5.07164 0.990872 > 99.4000 5.07205 1.00651 > 99.6000 5.07256 1.02346 > 99.8000 5.07107 0.986439 > 100. 5.06931 1.03009 > > $ tail force.xvg > 98.2000 -45.0273 > 98.4000 -24.1432 > 98.6000 -12.4043 > 98.8000 -14.3716 > 99. 2.42147 > 99.2000 4.56404 > 99.4000 -3.25742 > 99.6000 -11.7324 > 99.8000 6.78027 > 100. -15.0443 > > ### where it does start at -1.0 > > $ grep -v '[#|@]' coord.xvg |head > 0.5.05992 -1.09968 > 0.20005.05948 -0.473992 > 0.40005.05982 0.43101 > 0.60005.06017 0.77986 > 0.80005.0609 0.78875 > 1.5.06113 0.75552 > 1.20005.06151 0.750633 > 1.40005.06086 0.79958 > 1.60005.05976 0.821069 > 1.80005.05811 0.950296 > > ### > > pull_geometry= direction > pull_init1 = -1.0 > pull_vec1= 0 0 1 > > $ tail -n 30 coord.xvg|head -n 10 > 94.2000 5.04636 -1.00959 > 94.4000 5.04605 -1.09414 > 94.6000 5.04503 -1.09134 > 94.8000 5.0431 -1.10409 > 95. 5.04174 -1.05292 > 95.2000 5.
RE: [gmx-users] pull code with defined negative relative displacements
Hi, I would still say pull_geometry=direction would be the easiest solution for this case, but pull_geometry=position will probably do the same thing. Berk > Date: Sun, 15 Nov 2009 17:11:43 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] pull code with defined negative relative displacements > > Hi Berk, > > I do not mean the box 0, and I am aware about the pull distance > needing to be less than half of the smallest box length. Please allow > me describe a bit more rigorously what I need to avoid. I will use an > example that is totally fictitious, but is designed to emphasize the > bimodal sampling issue that is relevant to my actual study. > > 1. Imagine that one wants to calculate the PMF for a water molecule > along the normal to an asymmetric bilayer in which one leaflet is POPC > and the other is lipidA. > > 2. The free energy for that water residing 0.1 nm away from the > bilayer center in the POPC leaflet (call it -0.1 nm from the bilayer > center) needs to be calculated separately from the free energy for > that water residing 0.1 nm away from the bilayer center in the lipidA > leaflet (call it +0.1 nm from the bilayer center). > > 3. Let the force constant be 500 kJ/mol/nm^2 and let the user apply > pull_geometry=distance and pull_init1=0.1 while starting the replica > at 0.1 nm from the bilayer center in two simulations where one takes > (a) a starting water position that is 0.1 nm toward the POPC > headgroups and the other takes (b) a starting position of the water to > be 0.1 nm toward the lipidA headgroups. > > 4. I posit that the probability distributions of the water about the > bilayer normal from simulations (a) and (b) in part 3 above will > converge to the same distribution and that this distribution will be > bimodal with one peak at -0.1 nm and one peak at +0.1 nm. This is > because the simulation that started at -0.1 (0.1 nm closer to the POPC > headgroups) will, even under the biasing force, infrequently cross the > bilayer center of mass and then be closer to the lipidA heagroups. At > this point. the direction of the applied force will the change to draw > the water toward the other possible location at +0.1 nm. > > 5a. For displacements >> 0.1 nm, this will not be a problem. > 5b. For larger force constants, this will not be a problem at 0.1 nm, > but will still be a problem for some closer centers of restraint. > > 6. pull_geometry=distance is entirely incompatible with this approach. > > 7. pull_geometry=position does appear to work. > > > Thanks for your patience, > Chris. > > -- original message -- > > Hi, > > Sorry, but I have no clue what you mean with sampling >0 > and how you would end up with a bimodal distribution. > > You don't mean the box 0, do you? > That is irrelevant. > What can be a problem is that you pull distance should not be more > than half the box length. > > Berk > > > Date: Sun, 15 Nov 2009 12:33:30 -0500 > > From: chris.neale at utoronto.ca > > To: gmx-users at gromacs.org > > Subject: [gmx-users] pull code with defined negative relative displacements > > > > > 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. > > > > Agreed, although this will not work when the force constant is not > > strong enough to inhibit any sampling >0 -- wherein the distribution > > about 0 would become bimodal and this is something that I can not > > allow. > > > > As far as I can tell, pull_geometry=position, pull_init1<0, and > > pull_vec1=0 0 0 is the solution, as per my previous message. > > > > Thank you, > > Chris. > > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/-- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] pull code with defined negative relative displacements
Hi, Sorry, but I have no clue what you mean with sampling >0 and how you would end up with a bimodal distribution. You don't mean the box 0, do you? That is irrelevant. What can be a problem is that you pull distance should not be more than half the box length. Berk > Date: Sun, 15 Nov 2009 12:33:30 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] pull code with defined negative relative displacements > > > 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. > > Agreed, although this will not work when the force constant is not > strong enough to inhibit any sampling >0 -- wherein the distribution > about 0 would become bimodal and this is something that I can not allow. > > As far as I can tell, pull_geometry=position, pull_init1<0, and > pull_vec1=0 0 0 is the solution, as per my previous message. > > Thank you, > Chris. > > > > -- > gmx-users mailing listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] pull code with defined negative relative displacements
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: g...@hotmail.com To: gmx-users@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.ne...@utoronto.ca > To: gmx-users@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
RE: [gmx-users] pull code with defined negative relative displacements
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.ne...@utoronto.ca > To: gmx-users@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 compl
Re: [gmx-users] pull code with defined negative relative displacements
Berk Hess wrote: Hi, You should use pull_geometry=direction. distances don't get negative. I think this presents a problem if one is intending to use g_wham to calculate PMF from the umbrella sampling protocol. When using direction for pull_geometry, g_wham fails with a fatal error: --- Program g_wham, VERSION 4.0.5 Source code file: gmx_wham.c, line: 1337 Fatal error: Pull geometry direction not supported --- -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] pull code with defined negative relative displacements
Hi, You should use pull_geometry=direction. distances don't get negative. Berk > Date: Sat, 14 Nov 2009 09:21:39 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@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 (-1.00)" > > 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. 4.9343 -1.02019 > 660.0001 4.91454 -0.949747 > > force.xvg: > 610. -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 listgmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
