Thanks to ur quick response Would you please shed some light on my query no. 1 about the box size. Please go through that.
On Thu, May 10, 2018 at 5:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/10/18 1:24 AM, Rakesh Mishra wrote: > >> Dear Justin, >> >> I have discussed a lot regarding the pulling of dsRNA/dsDNA using gromacs >> about your protocol. Thanks for those discussion. >> But I faced two more basic problem in gromacs. >> >> 1- I need double size box if I need to pull half distance of box (Which >> makes time demanding ). >> Eg. let I want to pull DNA of length 34 Angstroms (3.4 nm) to 68 >> Angstroms (6.8 nm) along X direction. >> Then I need to make the box of the size just double of 6.8 nm i.e >> we need to box that must be extended in the pulling direction of the size >> 13. 6 nm. >> And then it needs lots of time to simulate compare to if I use >> other >> simulation tool for pulling like NAMD or Amber, where no need to make the >> box size double >> then the given pulling distance. Then Why Gromacs should be used >> for >> pulling . >> > > Use whatever software you like. No one says you have to use GROMACS :) > > 2- And I use constant velocity pulling with distance increasing. Then Its >> not possible to get variation of force/distance . It just gives linear >> variation like straight line with force. >> Yes, it gives basically variation of force with the time . >> > > Forces are in pullf.xvg and the displacement is in pullx.xvg. You can > easily plot force vs. distance from these two files. > > 3- But suppose we want get force versus stretch(extension) curve then how >> to do constant force pulling like constant velocity. >> > > There is an option of constant force pulling you can set in the .mdp file, > but it won't be useful to plot force vs. displacement/extension in this > case because the force is, by definition, constant. > > >> 4- Should we use NAMD for simple force versus extension curve . >> > > NAMD can do this kind of simulation if you prefer, but you can certainly > do it with GROMACS. > > -Justin > > My above 1-2-3 questions are important for me as a gromacs user. If >> possible please ans, I will be great full to you. >> >> >> >> On Fri, Feb 16, 2018 at 12:40 PM, Rakesh Mishra <rockin...@gmail.com> >> wrote: >> >> Dear Justin thanks for detail. >>> >>> Initially my system was positioned along the x direction. final >>> structure, >>> that we got After 10 ns generation for pulling >>> that system is slightly tilts toward the z direction but not exactly. >>> Please find the attache snapshot of tilted picture. >>> In this picture, I am trying to pull the left side end (in the downward z >>> direction),which is close to the z axis. >>> >>> >>> >>> On Thu, Feb 15, 2018 at 7:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> On 2/15/18 4:13 AM, Rakesh Mishra wrote: >>>> >>>> Dear Justin thanks for your advise. >>>>> >>>>> I will check for longer run for getting response according to you. >>>>> >>>>> >>>>> I would like to explain my system,which is siRNA of chain A and B. >>>>> Here, after doing all formalities, I had run 10 ns then try to apply >>>>> the >>>>> pull protocol. >>>>> >>>>> See, here for pulling this system, I have restricted 1st residue of >>>>> chain-A, and pulling last ( 22th) >>>>> residue of chain-B, which is at the same side end just below the 1st >>>>> residue of chain-A. >>>>> ( means, both reference and pull groups are at the same end side ). >>>>> >>>>> Note- I am pulling this 22th residue of chain-B in the downward (-z) >>>>> direction with negative rate. >>>>> ( here pull group is below from the reference group) >>>>> >>>>> I also followed your advise to pull with negative rate with high >>>>> spring >>>>> constant. But in this case also, >>>>> system is not moving in the downwards (-z ) direction. >>>>> >>>>> Interesting- >>>>> But the most interesting case is that for the same system just >>>>> discussed >>>>> above, when I am >>>>> applying pulling code with + rate even with smaller spring constant, >>>>> then >>>>> system is moving in >>>>> downward (-z) direction. While In my thinking, because I have given >>>>> +rate, >>>>> so it should move in >>>>> the + z direction. So, could it be possible that there is one thing >>>>> that >>>>> can also matter , >>>>> i.e. whether, pull group is below and reference group is above . >>>>> >>>>> Because in the same system, when I pull 22the residue of chain-A w.r.t >>>>> reference residue 1 of chain-B >>>>> (which is slightly below from the pull residue 22th of chain-A) with >>>>> the >>>>> same +rate and spring constant. >>>>> In this case pull group moves in the + z direction (upward), which I >>>>> expect >>>>> ( note- here pull group is >>>>> slightly above from the reference group) >>>>> >>>>> So, this contradiction with effect based on the end side pulling and >>>>> posing >>>>> of reference and pull groups >>>>> is making it surprise and trouble. >>>>> >>>>> How is the RNA oriented? Is the z-axis coincident with the helical >>>> axis? >>>> If so, that's a poor choice for a reaction coordinate and you should >>>> choose >>>> a different axis, orthogonal to the helix. Or just pull in all >>>> dimensions >>>> so that it's the total COM distance between the base pair. Remember, the >>>> tutorial is a special case in which a one-dimension pull made sense due >>>> to >>>> the inherent geometry of the unidirectional growth model of amyloid >>>> fibrils. Do not assume that all system should be treated this way. >>>> >>>> The negative pull rate means "bring the two specified groups together" >>>> not necessarily "pull along -z" so be sure your orientation convention >>>> aligns with what you're trying to do. >>>> >>>> -Justin >>>> >>>> >>>> >>>>> >>>>> On Wed, Feb 14, 2018 at 7:53 PM, Justin Lemkul <jalem...@vt.edu> >>>>> wrote: >>>>> >>>>> >>>>> On 2/14/18 7:31 AM, Rakesh Mishra wrote: >>>>>> >>>>>> Dear Justin, >>>>>> >>>>>>> Can you explain something regarding this issue. >>>>>>> >>>>>>> I couldn't get resolve one problem. Though now I am able to make >>>>>>> restrict (immobile ) >>>>>>> the needed residue and pulled another one. >>>>>>> But the contradiction that i am facing is that, when I am pulling >>>>>>> with >>>>>>> -rate (in negative z direction, as I want to pull >>>>>>> the residue in the negative Z direction of box ) given below. >>>>>>> Still there we see that pulling group is not moving the -ve >>>>>>> direction >>>>>>> of >>>>>>> z. >>>>>>> >>>>>>> Your settings are right, so either you need a larger force constant >>>>>>> to >>>>>>> >>>>>> induce the motion or you need to wait longer for the restoring forces >>>>>> in >>>>>> the system (whatever they are) to be overcome by the biasing >>>>>> potential. >>>>>> >>>>>> -Justin >>>>>> >>>>>> >>>>>> pull = yes >>>>>> >>>>>>> pull_ngroups = 2 >>>>>>> pull_ncoords = 1 >>>>>>> pull_group1_name = chain-A-start >>>>>>> pull_group2_name = chain-B-end >>>>>>> pull_coord1_type = umbrella ; harmonic biasing force >>>>>>> pull_coord1_geometry = distance ; simple distance increase >>>>>>> pull_coord1_groups = 1 2 >>>>>>> pull_coord1_dim = N N Y >>>>>>> pull_coord1_rate = -0.01 ; 0.01 nm per ps = 10 >>>>>>> per 1 >>>>>>> ns >>>>>>> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 >>>>>>> pull_coord1_start = yes ; define initial COM >>>>>>> distance >>>>>>> 0 >>>>>>> >>>>>>> >>>>>>> Best >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Feb 6, 2018 at 1:54 PM, Rakesh Mishra <rockin...@gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>> Thank you very much Justin. >>>>>>> >>>>>>> Here it is working but having some problem. >>>>>>>> pull_group2_name = chain_B35 is moving in the + z direction & >>>>>>>> pull_group4_name= chain_B26 is moving oppositely in the -z >>>>>>>> direction >>>>>>>> While I have given pull in +z direction for both the above group. >>>>>>>> >>>>>>>> Note - pull_group1_name = chain_A8 and pull_group3_name = >>>>>>>> chain_A17 >>>>>>>> are >>>>>>>> immobile here as well as acting as reference. >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul <jalem...@vt.edu> >>>>>>>> wrote: >>>>>>>> >>>>>>>> >>>>>>>> On 2/1/18 7:59 AM, Rakesh Mishra wrote: >>>>>>>> >>>>>>>>> Dear Justin >>>>>>>>> >>>>>>>>> Here I am applying pull for two groups with respect to two >>>>>>>>>> reference >>>>>>>>>> group >>>>>>>>>> as following. >>>>>>>>>> ; Pull code >>>>>>>>>> pull = yes >>>>>>>>>> pull_ngroups = 4 >>>>>>>>>> pull_ncoords = 1 >>>>>>>>>> pull_group1_name = chain_A8 (reference also immobile ) >>>>>>>>>> pull_group2_name = chain_B35 (pulling group) >>>>>>>>>> pull_group3_name = chain_A17 (reference also immobile) >>>>>>>>>> pull_group4_name = chain_B26 (pulling) >>>>>>>>>> pull_coord1_type = umbrella ; harmonic biasing force >>>>>>>>>> pull_coord1_geometry = distance ; simple distance increase >>>>>>>>>> pull_coord1_groups = 1 2 >>>>>>>>>> pull_coord1_dim = N N Y >>>>>>>>>> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm >>>>>>>>>> per 1 >>>>>>>>>> ns >>>>>>>>>> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 >>>>>>>>>> pull_coord1_start = yes ; define initial COM >>>>>>>>>> distance >>>>>>>>>> >>>>>>>>>> 0 >>>>>>>>>>> >>>>>>>>>>> In above protocol I want to make two reference group as >>>>>>>>>> 1-chain_A8 2- chain_A17 >>>>>>>>>> and two pull group. >>>>>>>>>> 1- chain_B35 2- chain_B26 >>>>>>>>>> >>>>>>>>>> You've defined four groups but then only used two, so you only get >>>>>>>>>> the >>>>>>>>>> >>>>>>>>>> effect of one reaction coordinate. >>>>>>>>> >>>>>>>>> What you need to do is define the pull settings for all reaction >>>>>>>>> coordinates simultaneously, e.g.: >>>>>>>>> >>>>>>>>> pull = yes >>>>>>>>> pull_ngroups = 4 >>>>>>>>> pull_ncoords = 2 >>>>>>>>> pull_group1_name = chain_A8 >>>>>>>>> pull_group2_name = chain_B35 >>>>>>>>> pull_group3_name = chain_A17 >>>>>>>>> pull_group4_name = chain_B26 >>>>>>>>> ; definition of reaction coordinate 1, groups 1-2 >>>>>>>>> pull_coord1_type = umbrella >>>>>>>>> pull_coord1_geometry = distance >>>>>>>>> pull_coord1_groups = 1 2 >>>>>>>>> pull_coord1_dim = N N Y >>>>>>>>> pull_coord1_rate = 0.01 >>>>>>>>> pull_coord1_k = 1000 >>>>>>>>> pull_coord1_start = yes >>>>>>>>> ; definition of reaction coordinate 2, groups 3-4 >>>>>>>>> pull_coord2_type = umbrella >>>>>>>>> pull_coord2_geometry = distance >>>>>>>>> pull_coord2_groups = 3 4 >>>>>>>>> pull_coord2_dim = N N Y >>>>>>>>> pull_coord2_rate = 0.01 >>>>>>>>> pull_coord2_k = 1000 >>>>>>>>> pull_coord2_start = yes >>>>>>>>> >>>>>>>>> Note that above I changed pull_ncoords to be set to 2, because you >>>>>>>>> want >>>>>>>>> two reaction coordinates. Then just specify the sett >>>>>>>>> <https://maps.google.com/?q=n+coordinates.+Then+just+specify >>>>>>>>> +the+sett&entry=gmail&source=g>ings >>>>>>>>> >>>>>>>>> for each one, >>>>>>>>> calling the appropriate groups by their assigned n >>>>>>>>> <https://maps.google.com/?q=he+appropriate+groups+by+their+assigned+n&entry=gmail&source=g> >>>>>>>>> umbers. >>>>>>>>> >>>>>>>>> -Justin >>>>>>>>> >>>>>>>>> -- >>>>>>>>> ================================================== >>>>>>>>> >>>>>>>>> Justin A. Lemkul, Ph.D. >>>>>>>>> Assistant Professor >>>>>>>>> Virginia Tech Department of Biochemistry >>>>>>>>> >>>>>>>>> 303 Engel Hall >>>>>>>>> 340 West Campus Dr. >>>>>>>>> Blacksburg, VA 24061 >>>>>>>>> >>>>>>>>> jalem...@vt.edu | (540) 231-3129 >>>>>>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>>>>>>>> >>>>>>>>> ================================================== >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Gromacs Users mailing list >>>>>>>>> >>>>>>>>> * Please search the archive at http://www.gromacs.org/Support >>>>>>>>> /Mailing_Lists/GMX-Users_List before posting! >>>>>>>>> >>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>>>> >>>>>>>>> * For (un)subscribe requests visit >>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>>>> or >>>>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>> * Rakesh Kumar Mishra* >>>>>>>> * (RA)CSD SINP Kolkata, India* >>>>>>>> >>>>>>>> *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> * >>>>>>>> >>>>>>>> *Phone n. +91 9473662491 <094736%2062491>, +91877749632* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>> >>>>>> ================================================== >>>>>> >>>>>> Justin A. Lemkul, Ph.D. >>>>>> Assistant Professor >>>>>> Virginia Tech Department of Biochemistry >>>>>> >>>>>> 303 Engel Hall >>>>>> 340 West Campus Dr. >>>>>> Blacksburg, VA 24061 >>>>>> >>>>>> jalem...@vt.edu | (540) 231-3129 >>>>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>>>>> >>>>>> ================================================== >>>>>> >>>>>> -- >>>>>> Gromacs Users mailing list >>>>>> >>>>>> * Please search the archive at http://www.gromacs.org/Support >>>>>> /Mailing_Lists/GMX-Users_List before posting! >>>>>> >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>>> * For (un)subscribe requests visit >>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>> >>>>>> >>>>>> >>>>> -- >>>> ================================================== >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Assistant Professor >>>> Virginia Tech Department of Biochemistry >>>> >>>> 303 Engel Hall >>>> 340 West Campus Dr. >>>> Blacksburg, VA 24061 >>>> >>>> jalem...@vt.edu | (540) 231-3129 >>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>>> >>>> ================================================== >>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at http://www.gromacs.org/Support >>>> /Mailing_Lists/GMX-Users_List before posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> >>> >>> -- >>> * Rakesh Kumar Mishra* >>> * (RA)CSD SINP Kolkata, India* >>> >>> *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> * >>> >>> *Phone n. +91 9473662491, +91877749632* >>> >>> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- * Rakesh Kumar Mishra* * (RA)CSD SINP Kolkata, India* *E-mail - rakesh.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> * *Phone n. +91 9473662491, +91877749632* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.