Dear Thomas, Thanks a lot again for great reply. Please clarify this also,
>> If one uses only 'Y N N' B would only move along the x-axis due to the pull, but could move freely in the yz-plane >>You never want to use the pull-code and 'pull_dim = N N N' >>This would mean that there is no force acting between your two groups. Then one could have skipped using the pull-code... So keeping Y N N will allow free movement in yz plane. So if I want A B to move freely in xyz but just keep them separated by some distance with spring const (just like two balloons tied to each other flying in air). Sorry confused. In AMBER I remember I did once methane-methane interaction, just distance based umbrella sampling. But there I did not provide any direction. So should it not be N N N in Gromacs if I want to allow them freely move in xyz. thanks, On Fri, May 31, 2013 at 8:53 PM, Thomas Schlesier <schl...@uni-mainz.de>wrote: > For comments to your questions see below. > > More general: (somewhat longer than i wanted. Hope you find some answers > here) > > Imagine two interacting particles A and B which are alinged to the x-axis. > We take A as the reference group, B as pulled group and put the origin of > the umbrella potential on top of B (pull_start=yes). > Simulation starts -> A and B moves. > Pull-code step: From A we calculate the new position of the umbrella > potential, this is unequal to B, since B moved and our reference point move. > Now we have a force acting on B, 'pull_dim' controls in which directions > the force acts. With 'Y Y Y' B is pulled towards the origin of the umbrella > potential (and with this to the position it should have relative to A). > If one uses only 'Y N N' B would only move along the x-axis due to the > pull, but could move freely in the yz-plane. In the end one would get a > structure where A and B have the right distance in the x-axis but are miles > away from each other in the yz-plane. > > Now imagine we pull B away from A. Since MD simulations normally separete > the movement of the center of mass of the system, it would look like A and > B would move away from a middle point. > > (Interchanging A and B should give the same results). > > > Think in your case (doing umbrella sampling) the mdp-file you suggested > would be most appropiate (with 'pull_start=yes' and 'pull_ngroups=1'). This > gives you a potential which fixes the distance between the two proteins. > One thing you should be aware is that if you restrain the distance in 3d, > you have to account for entropic effects (see also the GROMACS manual). If > you restrain the system only in one direction, these don't arise. Think > this is the reason why one sees some work with umbrella sampling were the > restraint works only in one direction. > > > Am 31.05.2013 17:20, schrieb gmx-users-requ...@gromacs.org: > > Dear Thomas, >> >> Thanks a lot for your time and nice explanation. I was not able to get >> specially the pull_start flag but now its quite clear. >> >> I feel sorry, that should be pull_dim = N N N in my case. Also I will be >> much thankful if you please can help me to make understand following: >> > > STOP!!! > You never want to use the pull-code and 'pull_dim = N N N' > This would mean that there is no force acting between your two groups. > Then one could have skipped using the pull-code... > > > >> 1) >> >>> >>If you do a pulling simulation, there can be reason for chosing the >>>> >>> groups (protein = reference , ligand = pulled group, since we want to >> pull >> it away) >> >> This indeed is correct but I am not able to get depth of this. I mean to >> say lets keep ligand as a reference and protein as pulled group then yes >> it >> sounds stupid but I am not able to provide a reason myself why we can not >> keep ligand as reference and pull protein rather !! >> > > Think this setup should also work. For some simple systems i imagine it > should give identical results. > For complex system i would also think so. But i can't comment on this with > actual expirience. The dimer systems which i investigated were symmetric... > > > > >> >> 2) >> >> > >3) And also what should be pull_ngroups because if there is no >>>> >>>>> >> >reference group then it should be 2 >>>>> >>>> >> >>>> >>> >Better use a reference group -> pull_ngroups = 1 >>> >> You don't want to pull in absolute coordinates, when your system can >> rotate.. >> >> I am not able to understand this part. Can you please provide some example >> so that it makes easier to understand this >> > > Imagine only a single protein which you want to unfold. In an equilibrium > simulation the protein can freely rotate in the box. If we use the > N-terminus as the reference group and the C-terminus a the pulled group, > the origin of the umbrella potential will always be updated and will > account for movement of the N-terminus (reference group). > If one would pull in absolute coordinates, one would need to give the > position of the umbrella potential in absolute space. The molecule can > move, but the origin of the potential will always stay fixed at one place. > Think in the end this would be equal to an position restraint of said group. > If one would want to restrain the distance of two groups in such a way, > one would need two umbrella potentials. But since these would be equal to > two position restraints, there would be no coupling between the two. I > mean, if both groups move around but would have the same distance it should > be ok since the distance is fine. But both umbrella potential would pull > each group back to the initial position. > > > >> >> Much thanks again, >> >> >> regards, >> Jiom >> >> >> >> >> On Fri, May 31, 2013 at 1:21 PM, Thomas Schlesier<schl...@uni-mainz.de** >> >wrote: >> >> >Look also into the manual. But the tutorial is a nice place to start. >>> >For further comments see below: >>> > >>> > >>> > Dear Lloyd, >>> >>>> >> >>>> >>I have read that but my system is different >>>> >> >>>> >>regards, >>>> >> >>>> >> >>>> >>On Thu, May 30, 2013 at 8:28 PM, lloyd riggs<lloyd.ri...@gmx.ch> >>>> wrote: >>>> >> >>>> >> >Dear Jiom, >>>> >>>>> >>> > >>>>>> >>> >Look at justines tutorial, there's example pull .mdp. >>>>>> >>> > >>>>>> >>> >Stephan Watkins >>>>>> >>> > >>>>>> >>>>> >>> >>>>> >>>> >> >>>> >>> > > >>> >>>> >>> >>>>> >>>>>> >>> >I want to do Umbrella sampling between two different polymers (A >>>>>> and B) >>>>>> >>> >interacting with each other with starting configuration >>>>>> separated by >>>>>> >>>>> >>>some >>>>> >>>>>> >>> >distance and I am trying to bring them closer. >>>>>> >>> > >>>>>> >>> >I have some queries regarding pull inputs: (this is for to run a >>>>>> >>>>> >>>umbrella >>>>> >>>>>> >>> >sampling at some distance) >>>>>> >>> > >>>>>> >>> >pull = umbrella >>>>>> >>> >pull_geometry = distance >>>>>> >>> >pull_dim = Y Y Y >>>>>> >>> >pull_start = ??? >>>>>> >>> >pull_ngroups = 2? >>>>>> >>> >pull_group0 = polymer_B >>>>>> >>> >pull_group1 = polymer_A >>>>>> >>> >pull_init1 = 0 >>>>>> >>> >pull_rate1 = 0.0 >>>>>> >>> > >>>>>> >>> > >>>>>> >>> >please suggest for following: >>>>>> >>> > >>>>>> >>> >1) pull_dim I have set to Y Y Y: Is this correct I do not want >>>>>> to make >>>>>> >>> >it interact with some directional vector >>>>>> >>>>> >>> >>>>> >>>> >> >>>> >>> >I don't really understand the question. If you use 'pull_dim = Y Y Y' >>> the >>> >pulling potential acts in all 3 dimensions, if you use 'pull_dim = Y N >>> N' >>> >the pulling potential acts only in the X direction and your two groups >>> an >>> >move freely in the YZ-plane. >>> > >>> > >>> > > >>> >>>> >>> >2) Which should be group0 or group1, in other words should I pull >>>>>> both >>>>>> >>> >together or how I should decide which one should be reference and >>>>>> >>> >which to be pulled as both are different polymers? >>>>>> >>>>> >>> >>>>> >>>> >>Depends on what you want to do. Easiest way would be define one >>>> polymer a >>>> >>> >group0/reference group and the other as group1/pulled group. System >>> >shouldn't care about which polymer is which group. >>> >If you do a pulling simulation, there can be reason for chosing the >>> groups >>> >(protein = reference , ligand = pulled group, since we want to pull it >>> away) >>> > >>> > >>> > > >>> >>>> >>> >3) And also what should be pull_ngroups because if there is no >>>>>> >>> >reference group then it should be 2 >>>>>> >>>>> >>> >>>>> >>>> >>Better use a reference group -> pull_ngroups = 1 >>>> >>> >You don't want to pull in absolute coordinates, when your system can >>> >rotate... >>> > >>> > >>> > > >>> >>>> >>> >4) I am not able to understand pull_start option with pull_init1. >>>>>> In >>>>>> >>> >this case if it is set to yes and 0.0 respectively then does >>>>>> that mean >>>>>> >>> >this combination is equivalent to pull_start = No if I just >>>>>> assume >>>>>> >>> >pull_init1 does not have any default value (which is 0.0); not >>>>>> >>> >existing >>>>>> >>>>> >>> >>>>> >>>> >> From the setup which you have written above: >>>> >>> >polymer_B is the reference group. the origin of the pulling potential is >>> >at 'pull_init1' (a length) along the vector which goes from polymer_B to >>> >polymer_A (sine you use pull_geometry = distance). >>> >If you set pull_init1=0 and pull_start=no, polymer_A will crash into >>> >polymer_B (since the origin of the umbrella potential is directly at the >>> >center of mass of polymer_B). >>> >If you set pull_init1=0 and pull_start=yes, GROMACS adds the distance >>> >between polymer_B and A to pull_init1 (-> so pull_init1 is now greater >>> than >>> >0.0). Now the origin of the umbrella potential is at the center of mass >>> of >>> >polymer_A. -> A is restrainted to a certian distance of B. >>> > >>> > > >>> >>>> >>> >5) Also finally where are upper and lower bounds defined. pull_k1 = >>>>>> >>> >1000 is harmonic applied to some equilibrium distance value. How >>>>>> this >>>>>> >>> >distance is taken by the programme (or it is just the starting >>>>>> >>> >distance taken between two groups) and what are the ?? values >>>>>> >>>>> >>> >>>>> >>>>>> >>> >defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is >>>>>> >>> >assumed equilibrium value and r1 is lower and r4 is upper value >>>>>> which >>>>>> >>> >defines shape of potential) >>>>>> >>>>> >>> >>>>> >>>> >>The umbrella potential is a simple harmonic potential (so no fancy >>>> stuff >>>> >>> >as in AMBER) with >>> >V = 1/2 k x^2 >>> >where x is the violation of the equilibrium distance. >>> >For your setup >>> >V = 1/2 (pull_init1 - distance(B-A))^2 >>> >where distance(B-A) means the distance between both polymers. >>> > >>> > >>> >Greetings >>> >Thomas >>> >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. 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