Dear Thomas, >> 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.
Sorry am wrong that should be Y Y Y in Gromcacs! for such case regards, On Fri, May 31, 2013 at 10:03 PM, gromacs query <gromacsqu...@gmail.com>wrote: > 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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