Re: [gmx-users] pull code - constraint pulling - forces are zeros
Hi, I believe there is no force output for constraint pulling. Try umbrella. Erik On Mar 18, 2013, at 3:28 PM, raghav singh wrote: Hello Fellow Users, I am trying to pull a DNA molecule. I have fixed one end and trying to pull the other one using this .mdp file.. force output is all zeros. I have tried going through the user-list but have not found any solution yet. I am using gmx-version 4.5.5. Any idea why is it happening.?? below is the mdp file i am using. Thank you Raghav ## title = constraint pulling simulation define = -DPOSRES ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 2; 1ns nstcomm = 10 ; Output parameters nstxout = 100 ; every 10 ps nstvout = 100 nstfout = 20 nstxtcout = 20 ; every 1 ps nstenergy = 20 energygrps = DNA Water_and_ions ; Bond parameters constraint_algorithm= lincs lincs_iter = 1 lincs_order = 4 constraints = all-bonds continuation= no ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = DNA Water_and_ions tau_t = 0.1 0.1 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = yes ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= constraint pull_geometry = distance ; simple distance increase pull_dim= N Y N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Fixed pull_group1 = Pull pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 500 ### -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Pull code, Velocity distribution
Hello, Sorry for bothering you with the same question but just want to make sure that I am getting my results correctly. I run simulations where two blocks of ice are in a sliding contact for 5 ns (using pull code). As an output of the simulation I have pullf.xvg file which I use for 'g_analyze -f pullf.xvg' command and assume that the average force it prints is the average pulling force calculated with the U = 1/2K(vt-(x-x0))^2 harmonic potential. Sorry again for double checking! Cheers, Nino From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Friday, November 02, 2012 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Pull code, Velocity distribution On 11/2/12 10:52 AM, Samadashvili Nino wrote: Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? This should be correct. I am using following parameters: pull = umbrella pull_geometry= direction_periodic pull_dim= Y Y Y pull_start = yes pull_ngroups = 1 pull_group0= ICE_A pull_group1= ICE_B pull_pbcatom0 = 0 pull_pbcatom1 = 0 pull_vec1 = 1 0 0 pull_rate1 = 0.004 pull_k1 = 1 Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B? Yes. Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the distribution plot calculated from the coordinates and they dont match. The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs? How what is calculated? How are you creating your own distributions from the coordinates? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] Pull code, Velocity distribution
Dear Justin, Thank you for your fast reply. I found out the difference between the plots so no question about the velocity distribution. Cheers, Nino From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Friday, November 02, 2012 5:04 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Pull code, Velocity distribution On 11/2/12 10:52 AM, Samadashvili Nino wrote: Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? This should be correct. I am using following parameters: pull = umbrella pull_geometry= direction_periodic pull_dim= Y Y Y pull_start = yes pull_ngroups = 1 pull_group0= ICE_A pull_group1= ICE_B pull_pbcatom0 = 0 pull_pbcatom1 = 0 pull_vec1 = 1 0 0 pull_rate1 = 0.004 pull_k1 = 1 Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B? Yes. Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the distribution plot calculated from the coordinates and they dont match. The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs? How what is calculated? How are you creating your own distributions from the coordinates? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Pull code, Velocity distribution
On 11/2/12 10:52 AM, Samadashvili Nino wrote: Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pulling force obtained through U = 1/2K(vt-(x-x0))^2 harmonic potential? This should be correct. I am using following parameters: pull = umbrella pull_geometry= direction_periodic pull_dim= Y Y Y pull_start = yes pull_ngroups = 1 pull_group0= ICE_A pull_group1= ICE_B pull_pbcatom0 = 0 pull_pbcatom1 = 0 pull_vec1 = 1 0 0 pull_rate1 = 0.004 pull_k1 = 1 Since I have pull_start=yes, does it mean that the initial spring length is the COM distance between ICE_A and ICE_B? Yes. Another question is regarded to the velocity distribution. I used g_traj to plot the velocity distribution of my system which I compared with the distribution plot calculated from the coordinates and they dont match. The distribution calculated by Gromacs has a tail while my calculations don't show any. Could you please tell me how is it calculated in Gromacs? How what is calculated? How are you creating your own distributions from the coordinates? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)
On 2012-10-04 11:50, Emma Eriksson wrote: Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I run separate simulations with distances 0-4 nm constrained. I use pull_geometry = cylinder. The pull parameters are the following: pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DMPC pull_group1 = 2 pull_vec1 = 0 0 1 pull_init1 = x I have previously been using the same methodology in 4.0.5 without problems. When i run grompp in 4.5.5 I get the following error: Fatal error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310) The source of the first value, which should be the distance of pull group 1 is for me unknown. A value of ~4 is generated for all systems no matter what z distance is actually betwen the two groups (0-4 nm), so the value has no connection to the z distance between the groups. The second value is 0.5 times the x box length. I have read through pull.c, but I cannot find an explanation to why the x direction seems to be considered and not the z direction. When I run grompp with pull_geometry = distance or direction together with pull_dim = N N Y there is no problem. As I am not sure of the source of this error when running with cylinder I do not know if it is only related to the check or if the following simulation would be affected if I uncomment the check. Any suggestions to why this is happening and what I can do about it? Check the other pull_XXX values in mdout.mdp You have not specified all of them above, e.g. pull_direction? Thanks! Best regards, Emma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pull-code
Hi Thomas Many thanks for the reply again. At larger distances the two curves match up quite well. The curve from the reversible work theorem is better behaved and smoother but this could be solely due to statistics. I am slightly confused about your statement If the small circle moves between 0 and any value 0 everything should be fine. Do you not mean 0 and any value 0 ? Cheers Gavin Thomas Schlesier wrote: Hi Gavin, if i remember correctly it was a system about pulling a ligand from a binding pocket? To make the system simpler we have a big circle and in the middle a small circle. And we assume that the potential minimum for the interaction between both circles is when the small cirlce is in the middle of the large circle. Now we do the Umbrella sampling. For a window which is centered at a distance which is sligthly greater then 0, we will get problems. Assume small circle is sligthly shifted to the right. And the other windows are also in this dircetion. (- reaction coordinate goes from zero to the right dircetion) If the small circle moves between 0 and any value 0 everythig should be fine. But if the small circle moves to the left, we will also get a positive distance. Problem is from the above defined reaction coordinate it should be a negative distance. So we are counting the positive distances too much. To check this, you could use *g_dist* to calculate the distance for both molecules for the problematic windows. Then project the resulting vector onto your reaction coordinate. Then you should see the crossings between the right and left side. How do the two free energy curves compare for larger distances, where you can be sure, that you do not have this 'crossing problem'? Greetings Thomas - Hi all I am returning to a query I had a few weeks ago regarding a discrepancy between two free energy curves. One calculated using umbrella sampling, the other calculated via the reversible work theorem from the RDF. There is sufficient sampling of the dynamics in the RDF so this method is viable. Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y. The free energy curve from the pull-code method does not give me a minimum at the zero value of the order parameter whereas the RDF method does. Someone said before about double counting of positive distances at small values of the order parameter and therefore information is lost at very small distances. Is this correct? I am slightly concerned that my curves are not giving me the correct information involving a very important state in my reaction coordinate. Also when this dist restraint (which cannot be negative) is implemented are there issues with the normalisation of the histograms from g_wham? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pull-code
Hi Thomas I am sorry to bother you but if you could answer a few questions I have about how the pull-code works with respect to my system I would really appreciate it. My system is a liquid and I am trying to pull one substituent of one liquid molecule in a certain region of another liquid molecule using as I said earlier pull_geometry =dist and pull_dim =YYY. Also pull_start = no Say I have a window with pull_init=0 1) At the very start of the simulation the pullcode calculates the vector between the two groups? Is there anything particularly significant about this initial vector? Is this distance vector recalculated at every step? 2) Does it compare the distance vector an time t with that at time 0.? 3) Given the initial vector can this vector change (i.e. dierection) or does the distance between the two groups vary only along this vector (i.e. in a line) ? Cheers Gavin Thomas Schlesier wrote: Hi Gavin, if i remember correctly it was a system about pulling a ligand from a binding pocket? To make the system simpler we have a big circle and in the middle a small circle. And we assume that the potential minimum for the interaction between both circles is when the small cirlce is in the middle of the large circle. Now we do the Umbrella sampling. For a window which is centered at a distance which is sligthly greater then 0, we will get problems. Assume small circle is sligthly shifted to the right. And the other windows are also in this dircetion. (- reaction coordinate goes from zero to the right dircetion) If the small circle moves between 0 and any value 0 everythig should be fine. But if the small circle moves to the left, we will also get a positive distance. Problem is from the above defined reaction coordinate it should be a negative distance. So we are counting the positive distances too much. To check this, you could use *g_dist* to calculate the distance for both molecules for the problematic windows. Then project the resulting vector onto your reaction coordinate. Then you should see the crossings between the right and left side. How do the two free energy curves compare for larger distances, where you can be sure, that you do not have this 'crossing problem'? Greetings Thomas - Hi all I am returning to a query I had a few weeks ago regarding a discrepancy between two free energy curves. One calculated using umbrella sampling, the other calculated via the reversible work theorem from the RDF. There is sufficient sampling of the dynamics in the RDF so this method is viable. Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y. The free energy curve from the pull-code method does not give me a minimum at the zero value of the order parameter whereas the RDF method does. Someone said before about double counting of positive distances at small values of the order parameter and therefore information is lost at very small distances. Is this correct? I am slightly concerned that my curves are not giving me the correct information involving a very important state in my reaction coordinate. Also when this dist restraint (which cannot be negative) is implemented are there issues with the normalisation of the histograms from g_wham? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pull-code
Hello, I was following your argument but then doesnt pull_dim=Y Y Y mean it pulls in all directions at once? I use pull_dim=N N Y , or just 1 pull direction and it works. I might be wrong, but would be interesting if you got it to work like that for a small molecule. Stephan Watkins Original-Nachricht Datum: Fri, 17 Feb 2012 16:34:22 +0100 Von: Thomas Schlesier schl...@uni-mainz.de An: gmx-users@gromacs.org Betreff: [gmx-users] pull-code Hi Gavin, if i remember correctly it was a system about pulling a ligand from a binding pocket? To make the system simpler we have a big circle and in the middle a small circle. And we assume that the potential minimum for the interaction between both circles is when the small cirlce is in the middle of the large circle. Now we do the Umbrella sampling. For a window which is centered at a distance which is sligthly greater then 0, we will get problems. Assume small circle is sligthly shifted to the right. And the other windows are also in this dircetion. (- reaction coordinate goes from zero to the right dircetion) If the small circle moves between 0 and any value 0 everythig should be fine. But if the small circle moves to the left, we will also get a positive distance. Problem is from the above defined reaction coordinate it should be a negative distance. So we are counting the positive distances too much. To check this, you could use *g_dist* to calculate the distance for both molecules for the problematic windows. Then project the resulting vector onto your reaction coordinate. Then you should see the crossings between the right and left side. How do the two free energy curves compare for larger distances, where you can be sure, that you do not have this 'crossing problem'? Greetings Thomas - Hi all I am returning to a query I had a few weeks ago regarding a discrepancy between two free energy curves. One calculated using umbrella sampling, the other calculated via the reversible work theorem from the RDF. There is sufficient sampling of the dynamics in the RDF so this method is viable. Anyway in the pull-code I use pull_geometry = dist and pull_dim=Y Y Y. The free energy curve from the pull-code method does not give me a minimum at the zero value of the order parameter whereas the RDF method does. Someone said before about double counting of positive distances at small values of the order parameter and therefore information is lost at very small distances. Is this correct? I am slightly concerned that my curves are not giving me the correct information involving a very important state in my reaction coordinate. Also when this dist restraint (which cannot be negative) is implemented are there issues with the normalisation of the histograms from g_wham? Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://www.gmx.net/de/go/freephone/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pull code problem: between protofilaments
Dear Chris, Thank a lot for your reply. I am trying the pull code that you have suggested. And I would be more specific about the problem and code in my future mails. regards, Shilpi On 02/10/11, chris.ne...@utoronto.ca wrote: Dear Shilpi: Can you use something like this? pull = umbrella pull_geometry = position pull_dim = N N Y pull_vec1 = 0 0 0 pull_start = no pull_ngroups = 1 pull_group0 = PRO-1 pull_pbcatom0 = set this or use 0 pull_group1 = PRO-2 pull_pbcatom1 = set this or use 0 pull_init1 = 0 0 set initial value here for z-axis pull_rate1 = 0 pull_k1 = 500.0 pull_nstxout = 500 pull_nstfout = 500 The above is for umbrella sampling. If you want to do continuous pulling, then: pull_start = yes pull_rate1 = set the rate ### Also: Next time you post, please provide more specifics. For example, I suggested a .mdp file in specifics to you above and I bet it would have been harder for you to guess what I meant if I had just told you the general idea instead of pasting some .mdp options. Likewise, your initial post would have been clearer it you had copied and pasted the .mdp pull code section that you tried to use. Chris. -- original message -- Dear Gmx users, I am studying the interaction between the tubulin protofilaments arranged in parallel. For this operation, I have considered a tetramer and a dimer from two protofilaments respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in PRO-2. I want to move the dimer of PRO-2 over the tetramer of PRO-1 along the length of protofilaments in one axis only, keeping the PRO-1 fixed to its original position. I tried by assuming tetramer as 'reference group' and the dimer as 'pull group' in pull code but the system crashed. I have succeeded in separating two dimers in Z-axis by using 'distance' geometry. But this case is quite different, as the pulling is not face-to-face but rather a sliding movement over another protofilament. Here, the COM distance between the pull group (dimer of PRO-2) and reference group (tetramer of PRO-1) first decreases and then increases while it moves. How can I simulate this operation by using pull code? Thanks, best regards, Shilpi Chaurasia -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)
Dear Justin, Thanks a lot for your reply. Here I am providing the data and explaining the problem in detail: I hope that it will help you in understanding in a better way. Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as another, I want to separate 'ab' and 'cd'. Length of each dimer is 8 nm, so the tetramer (initial configuration) is approximately 16 nm and I have used a cubic box of 30 nm. Two groups (reference group and pull group) are decided on the basis of residue numbers forming 'ab' as reference grp and 'bc' as pull group by making an index file. I have verified that the initial configuration does not split across periodic boundaries, it is always inside the box throughout the simulation. Moreover, the initial distance is not equal to box vector. By g_dist , I have tried to calculate the distance between the two groups and it came out to be approx. 15 nm (Please have a look at the dist.xvg file at the end). Do you think that in the first ps time frame, should it get separated by 15 nm?? Please correct me if I have done anything wrong. By mistake, in my last mail I wrote that I need to pull along Y axis. In actual, it is Z-axis and I have used pull_dim N N Y. So it is just the mistake in writing the mail. Please let me know do you need any other data or parameters that I have used during this simulation. An early reply would me much appreciated. --- --- dist.xvg # This file was created Tue Sep 13 11:09:23 2011 # by the following command: # g_dist -f tub_pull.xtc -s tub_pull.tpr -n index.ndx # # g_dist is part of G R O M A C S: # # Giving Russians Opium May Alter Current Situation # @ title Distance @ xaxis label Time (ps) @ yaxis label Distance (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend |d| @ s1 legend d\sx\N @ s2 legend d\sy\N @ s3 legend d\sz\N 0.000 15.0342455 -0.7714367 -0.9718266 14.9829559 0.500 15.0345469 -0.7726345 -0.9766102 -14.9828863 1.000 15.0345631 -0.7665710 -0.9862967 -14.9825792 1.500 15.0343399 -0.7575226 -0.9916229 14.9824638 2.000 15.0335970 -0.7490749 -0.9957008 -14.9818726 2.500 15.0322971 -0.7446661 -0.9996347 -14.9805260 3.000 15.0341187 -0.7364883 -1.0029345 -14.9825373 3.500 15.0331717 -0.7328205 -1.0078001 14.9814405 4.000 15.0311899 -0.7334194 -1.0118599 14.9791489 4.500 15.0334759 -0.7351160 -1.0128736 14.9812908 5.000 15.0336533 -0.7327585 -1.0102243 14.9817638 5.500 15.0327044 -0.7342167 -1.0076447 14.9809132 6.000 15.0335188 -0.7365904 -1.0090990 -14.9815168 6.500 15.0296631 -0.7375288 -1.0111809 -14.9774609 7.000 15.0294476 -0.7318525 -1.0155020 -14.9772310 7.500 15.0322533 -0.7323456 -1.0173597 -14.9798965 8.000 15.0353861 -0.7333517 -1.0172930 14.9829950 8.500 15.0323915 -0.7285290 -1.0122719 14.9805660 9.000 15.0284719 -0.7241497 -1.0072327 14.9771843 9.500 15.0285101 -0.7232113 -1.0051012 14.9774113 10.000 15.0306396 -0.7257242 -1.0020084 14.9796333 10.500 15.0324621 -0.7242069 -0.9959688 14.9819384 11.000 15.0324860 -0.7183657 -0.9881392 -14.9827623 11.500 15.0308609 -0.7121477 -0.9848318 -14.9816465 12.000 15.0318832 -0.7091122 -0.9842033 14.9828577 12.500 15.0316772 -0.7063818 -0.9834919 -14.9828262 13.000 15.0291939 -0.7024584 -0.9846754 -14.9804420 13.500 15.0307999 -0.7052488 -0.9864941 14.9818020 14.000 15.0286407 -0.7049980 -0.9902172 14.9794016 14.500 15.0301456 -0.7010813 -0.9916439 -14.9810019 15.000 15.0305882 -0.6967783 -0.9922857 -14.9816036 15.500 15.0319242 -0.6941795 -0.9950562 14.9828815 16.000 15.0315027 -0.6892128 -0.9928131 14.9828358 16.500 15.0314274 -0.6889334 -0.9883585 -14.9830685 17.000 15.0296593 -0.6906672 -0.9852924 14.9814167 17.500 15.0277662 -0.6964712 -0.9844646 -14.9793034 18.000 15.0301647
Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)
Shilpi Chaurasia wrote: Dear Justin, Thanks a lot for your reply. Here I am providing the data and explaining the problem in detail: I hope that it will help you in understanding in a better way. Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as another, I want to separate 'ab' and 'cd'. Length of each dimer is 8 nm, so the tetramer (initial configuration) is approximately 16 nm and I have used a cubic box of 30 nm. Two groups (reference group and pull group) are decided on the basis of residue numbers forming 'ab' as reference grp and 'bc' as pull group by making an index file. I will assume you mean CD here. If your groups are AB and BC, then you'll certainly have problems. I have verified that the initial configuration does not split across periodic boundaries, it is always inside the box throughout the simulation. Moreover, the initial distance is not equal to box vector. By g_dist , I have tried to calculate the distance between the two groups and it came out to be approx. 15 nm (Please have a look at the dist.xvg file at the end). Do you think that in the first ps time frame, should it get separated by 15 nm?? Please correct me if I have done anything wrong. If the dimer truly is together, then I would think this distance is too large unless (1) it actually is actually split across PBC, (2) your size calculations are wrong, or (3) your index groups are wrong. In any case, I can see this being a problem. A distance of 15 nm is 50% of the box size, and as soon as separation occurs, your pulling reference distance will be greater than 50% of the box vector, which causes a periodic distance to be calculated. Either use the distance_periodic pulling geometry or use a larger box. See below for a few thoughts on the dist.xvg data. By mistake, in my last mail I wrote that I need to pull along Y axis. In actual, it is Z-axis and I have used pull_dim N N Y. So it is just the mistake in writing the mail. Please let me know do you need any other data or parameters that I have used during this simulation. It would also be useful to know what grompp printed as the reference distance at time t=0. Here's why I think periodicity is indeed an issue: 0.000 15.0342455 -0.7714367 -0.9718266 14.9829559 0.500 15.0345469 -0.7726345 -0.9766102 -14.9828863 Note that within 0.5 ps, the sign of the z-distance has changed but the magnitude is basically the same. This indicates to me that your dimer is dancing back and forth across a periodic boundary. The output of pullx.xvg would also be informative to confirm this phenomenon. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)
Shilpi Chaurasia wrote: I am trying to pull apart two dimers of tubulin protein joined together, to form two separate dimers by steered molecular dynamics using Pull code. The objective is to separate the dimers by pulling along one axis only (Y axis). I ran the simulation for 25 ps and it accomplished well but while visualizing the trajectory in VMD, in the very beginning (first frame), dimers are at distance which is much greater than expected. I expected that in first frame they should not have separated too much (i.e. in just 1 ps, they are at greater distance) I guess this is unusual. Please let me know where I am doing wrong? I have used the following pull code: Actual numbers would help. Is your initial configuration simply split across periodic boundaries? If the initial distance is roughly equivalent to one of the box vectors, then that's the case. Otherwise, please provide real data and check to make sure your pull groups are what you think they are. pull= umbrella pull_geometry = distance pull_dim= N N Y Note that you're not actually pulling along Y as you state above. Here, you're pulling along Z. Perhaps that's one issue. -Justin pull_start = yes pull_init1 = 0.0 pull_ngroups= 1 pull_group0 = dimer_ref ; reference group (based on index file) pull_group1 = dimer_pull ; pull group pull_rate1 = 0.1 pull_k1 = 1000 pull_nstfout= 10 pull_nstxout= 10 best regards, Shilpi Chaurasia -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
RE: [gmx-users] pull code
Hi Justin, As discussed earlier, I removed the restraints from lipids and used constraint force for pulling, I was able to pull the peptide to the lower leaf headgroups starting from 1.3nm above the upper leaf headgroups. Below is the pull code inputs i used: ; Pull code pull= constraint pull_geometry = direction pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.013 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 But going through the summary_distances.dat file i wasnt sure of the progression of COM distance between peptide and bilayer. The first conf.gro starts at 3.84685nm it goes on reducing till it reaches conf 322 1.0903 nm, at this point when i viewed the 322.gro file the peptide is approximately in center of the bilayer. From this point onwards distance keeps increasing and it reaches conf 500 at 2.864 nm. But viewing the gro. file in vmd from conf 328.. conf 500, the peptide is being pulled to the lower leaf headgroups. So the peptide was pulled to the lower leaf headgroup as expected but I am not sure with the progression. 0 3.8468513 1 3.8324797 2 3.8197916 . . . 322 1.0903752 . . 328 1.1572036 . . 498 2.8465521 499 2.8731604 500 2.8649662 From here i carried on to do umbrella simulations for 24 windows which i generated for 10ns each, below is the pull code which i used for umbrella samplingafter analysis PMF converges and looking at the histogram theres sufficient overlap between windows. But due to increase in progression after conf 322 till conf 500 some peaks in the histogram looks like written twice. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 10 February 2011 12:33 To: Gromacs Users' List Subject: Re: [gmx-users] pull code Poojari, Chetan wrote: Hi Justin, Thank you very much for your suggestions. I will use constraint force to force a peptide into a membrane with pulling for longer time. yes with POSRES_LIPID i am keeping the lipids rigid while pulling the peptide inside. Should the lipids be flexible while pulling?? If your lipids are completely rigid, then they will not be happy accommodating the introduction of a peptide into that environment. I am using pull_geometry = direction, In the tutorial mdp file you had commented saying cant get PMF with direction. So please can I know if this error of not getting PMF with direction fixed or with pull_geometry = distance will i be able to pull the peptide into membrane with still using pull direction pull_vec1 = 0.0 0.0 -1.0 You're not doing umbrella sampling, you're doing steered MD, which is a non-equilibrium process. Please read the tutorial carefully. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for GROMACS users Subject: Re: [gmx-users] pull code Poojari, Chetan wrote: Hi, I am using umbrella sampling to pull my peptide (peptide starting from above the lipid bilayer) into the hydrophobic core of the lipid bilayer. Following are my inputs i have used: title = Umbrella pulling simulation define = -DPOSRES_LIPID ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 1 . . ; Pull code pull= umbrella pull_geometry = direction pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 After running the this step: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr i get grompp output as such: Pull group natoms pbc atom distance at start reference at t=0 0 6656 3433 1 10553 -4.132-4.132 I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am using POPC lipids and distance between 2 adjacent headgroups seem to be around 4.2 nm. I want
Re: [gmx-users] pull code
Poojari, Chetan wrote: Hi Justin, As discussed earlier, I removed the restraints from lipids and used constraint force for pulling, I was able to pull the peptide to the lower leaf headgroups starting from 1.3nm above the upper leaf headgroups. Below is the pull code inputs i used: ; Pull code pull= constraint pull_geometry = direction pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.013 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 But going through the summary_distances.dat file i wasnt sure of the progression of COM distance between peptide and bilayer. The first conf.gro starts at 3.84685nm it goes on reducing till it reaches conf 322 1.0903 nm, at this point when i viewed the 322.gro file the peptide is approximately in center of the bilayer. From this point onwards distance keeps increasing and it reaches conf 500 at 2.864 nm. But viewing the gro. file in vmd from conf 328.. conf 500, the peptide is being pulled to the lower leaf headgroups. So the peptide was pulled to the lower leaf headgroup as expected but I am not sure with the progression. 0 3.8468513 1 3.8324797 2 3.8197916 . . . 322 1.0903752 . . 328 1.1572036 . . 498 2.8465521 499 2.8731604 500 2.8649662 From here i carried on to do umbrella simulations for 24 windows which i generated for 10ns each, below is the pull code which i used for umbrella samplingafter analysis PMF converges and looking at the histogram theres sufficient overlap between windows. But due to increase in progression after conf 322 till conf 500 some peaks in the histogram looks like written twice. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps You've got a scenario for which the tutorial's input files will not suffice for your purposes. The simple example in the tutorial is for a linear pull resulting in a continually increasing COM distance. In your case, you are starting at a relative positive COM displacement, and ending at a negative one (i.e., below the POPC COM). For this application, you'll need to use a different pull_geometry (probably position), and perhaps other options. There are examples in the list archive, if you spend some time searching. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 10 February 2011 12:33 To: Gromacs Users' List Subject: Re: [gmx-users] pull code Poojari, Chetan wrote: Hi Justin, Thank you very much for your suggestions. I will use constraint force to force a peptide into a membrane with pulling for longer time. yes with POSRES_LIPID i am keeping the lipids rigid while pulling the peptide inside. Should the lipids be flexible while pulling?? If your lipids are completely rigid, then they will not be happy accommodating the introduction of a peptide into that environment. I am using pull_geometry = direction, In the tutorial mdp file you had commented saying cant get PMF with direction. So please can I know if this error of not getting PMF with direction fixed or with pull_geometry = distance will i be able to pull the peptide into membrane with still using pull direction pull_vec1 = 0.0 0.0 -1.0 You're not doing umbrella sampling, you're doing steered MD, which is a non-equilibrium process. Please read the tutorial carefully. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for GROMACS users Subject: Re: [gmx-users] pull code Poojari, Chetan wrote: Hi, I am using umbrella sampling to pull my peptide (peptide starting from above the lipid bilayer) into the hydrophobic core of the lipid bilayer. Following are my inputs i have used: title = Umbrella pulling simulation define = -DPOSRES_LIPID ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 1 . . ; Pull code pull= umbrella pull_geometry = direction pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 ; 0.01 nm
RE: [gmx-users] pull code
Hi Justin, Thank you very much for your suggestions. I will use constraint force to force a peptide into a membrane with pulling for longer time. yes with POSRES_LIPID i am keeping the lipids rigid while pulling the peptide inside. Should the lipids be flexible while pulling?? I am using pull_geometry = direction, In the tutorial mdp file you had commented saying cant get PMF with direction. So please can I know if this error of not getting PMF with direction fixed or with pull_geometry = distance will i be able to pull the peptide into membrane with still using pull direction pull_vec1 = 0.0 0.0 -1.0 Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for GROMACS users Subject: Re: [gmx-users] pull code Poojari, Chetan wrote: Hi, I am using umbrella sampling to pull my peptide (peptide starting from above the lipid bilayer) into the hydrophobic core of the lipid bilayer. Following are my inputs i have used: title = Umbrella pulling simulation define = -DPOSRES_LIPID ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 1 . . ; Pull code pull= umbrella pull_geometry = direction pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 After running the this step: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr i get grompp output as such: Pull group natoms pbc atom distance at start reference at t=0 0 6656 3433 1 10553 -4.132-4.132 I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am using POPC lipids and distance between 2 adjacent headgroups seem to be around 4.2 nm. I want the peptide to be pulled into the bilayer till the lower leaf lipid headgroups, but the peptide is being pulled only till middle of the hydrophobic core of the bilayer. Please can I know what might be the problem ? Either you're (1) not pulling for sufficient time, (2) not pulling hard enough, or (3) the physical properties of the system don't allow for such a position. For (2), using a harmonic potential to try to force a peptide into a membrane is probably not a great idea. A constraint force is probably better. For (3), what does POSRES_LIPID refer to? Are you keeping the lipids too rigid by doing so? While viewing the conf.*gro file outputed from the traj. (after extracting the frames), i found few lipid molecules to be broken. Please can I know if there is a way to avoid these broken structures??? Is there a possibility that I am not able to pull the peptide into the lower leaf head group due to these broken lipid structures? Please become comfortable with the concept of periodic boundary conditions. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin Any suggestions will be helpful. Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org
Re: [gmx-users] pull code
Poojari, Chetan wrote: Hi Justin, Thank you very much for your suggestions. I will use constraint force to force a peptide into a membrane with pulling for longer time. yes with POSRES_LIPID i am keeping the lipids rigid while pulling the peptide inside. Should the lipids be flexible while pulling?? If your lipids are completely rigid, then they will not be happy accommodating the introduction of a peptide into that environment. I am using pull_geometry = direction, In the tutorial mdp file you had commented saying cant get PMF with direction. So please can I know if this error of not getting PMF with direction fixed or with pull_geometry = distance will i be able to pull the peptide into membrane with still using pull direction pull_vec1 = 0.0 0.0 -1.0 You're not doing umbrella sampling, you're doing steered MD, which is a non-equilibrium process. Please read the tutorial carefully. -Justin Kind regards, chetan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 09 February 2011 16:40 To: Discussion list for GROMACS users Subject: Re: [gmx-users] pull code Poojari, Chetan wrote: Hi, I am using umbrella sampling to pull my peptide (peptide starting from above the lipid bilayer) into the hydrophobic core of the lipid bilayer. Following are my inputs i have used: title = Umbrella pulling simulation define = -DPOSRES_LIPID ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 1 . . ; Pull code pull= umbrella pull_geometry = direction pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 After running the this step: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr i get grompp output as such: Pull group natoms pbc atom distance at start reference at t=0 0 6656 3433 1 10553 -4.132-4.132 I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am using POPC lipids and distance between 2 adjacent headgroups seem to be around 4.2 nm. I want the peptide to be pulled into the bilayer till the lower leaf lipid headgroups, but the peptide is being pulled only till middle of the hydrophobic core of the bilayer. Please can I know what might be the problem ? Either you're (1) not pulling for sufficient time, (2) not pulling hard enough, or (3) the physical properties of the system don't allow for such a position. For (2), using a harmonic potential to try to force a peptide into a membrane is probably not a great idea. A constraint force is probably better. For (3), what does POSRES_LIPID refer to? Are you keeping the lipids too rigid by doing so? While viewing the conf.*gro file outputed from the traj. (after extracting the frames), i found few lipid molecules to be broken. Please can I know if there is a way to avoid these broken structures??? Is there a possibility that I am not able to pull the peptide into the lower leaf head group due to these broken lipid structures? Please become comfortable with the concept of periodic boundary conditions. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin Any suggestions will be helpful. Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe
Re: [gmx-users] pull code
Poojari, Chetan wrote: Hi, I am using umbrella sampling to pull my peptide (peptide starting from above the lipid bilayer) into the hydrophobic core of the lipid bilayer. Following are my inputs i have used: title = Umbrella pulling simulation define = -DPOSRES_LIPID ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 1 . . ; Pull code pull= umbrella pull_geometry = direction pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = POPC pull_group1 = Protein pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 After running the this step: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr i get grompp output as such: Pull group natoms pbc atom distance at start reference at t=0 0 6656 3433 1 10553 -4.132-4.132 I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am using POPC lipids and distance between 2 adjacent headgroups seem to be around 4.2 nm. I want the peptide to be pulled into the bilayer till the lower leaf lipid headgroups, but the peptide is being pulled only till middle of the hydrophobic core of the bilayer. Please can I know what might be the problem ? Either you're (1) not pulling for sufficient time, (2) not pulling hard enough, or (3) the physical properties of the system don't allow for such a position. For (2), using a harmonic potential to try to force a peptide into a membrane is probably not a great idea. A constraint force is probably better. For (3), what does POSRES_LIPID refer to? Are you keeping the lipids too rigid by doing so? While viewing the conf.*gro file outputed from the traj. (after extracting the frames), i found few lipid molecules to be broken. Please can I know if there is a way to avoid these broken structures??? Is there a possibility that I am not able to pull the peptide into the lower leaf head group due to these broken lipid structures? Please become comfortable with the concept of periodic boundary conditions. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -Justin Any suggestions will be helpful. Kind regards, chetan. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] pull code absolute reference
bv07ay wrote: Hello, i am having trouble using the pull options in gromacs 4.0.4. i am simply trying to move a protein from the top of the box to a certain point in the center. i have had no luck using a constant pulling or umbrella pulling the error i receive is: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. here is my most recent .mdp pull options: ; PULL pull= umbrella pull_geometry= position ;pull_group0= pull_init1= 3.279 3.279 3.90 pull_group1= MID pull_dim= Y Y Y pull_k1= 50 is there a way to make my system have an absolute reference? or is there some other way of pulling it that has worked for others? The error message is related less to the pull options than it is to COM motion removal. For instance: http://lists.gromacs.org/pipermail/gmx-users/2009-April/041329.html http://lists.gromacs.org/pipermail/gmx-users/2006-July/022753.html If you search the mailing list archives you will find lots of related posts. I pulled those up immediately by searching: absolute reference pulling. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Hi Justin Thanks for your help. The two molecules are now moving together. I am however slightly confused about the parameters pull_rate1 and pull_k1. I want the molecules to come together very slowly therefore I would set the rate to be a very small value. How the does the force come into play and how should you decide on the best value? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks. If I use the pull_geometry = direction I would go for the following jus t to pull the molecules together in the z direction. pull= umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 pull_k1 = 1000 Does this seem reasonable? Also in the pull_rate what is meant by the Probably. Try it. 'rate of change of the reference position'? (Is it the position of the reference group, if so what if I don't want it to change?) It is the rate of change of the reference position, which is the position at the outset of the simulation. Your objective is to pull your two species together, right? I don't see why you wouldn't want it to change. You're not changing anything about pull_group0 (your reference group), since you aren't setting pull_rate0. Everything is applied to pull_group1 (hence _rate1, _k1, etc). -Justin Cheers Gavin -- 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
Gavin Melaugh wrote: Hi all I am commencing the initial stages for he calculation of potential of mean force of bringing together two cage molecules. I am following the tutorial in such an exercise at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html In contrast to the tutorial I want to bring the two molecules together along the z axis. I have generated an initial configuration in which the COMs of the two molecules are 5.07 nm apart. In the tutorial to separate a substrate from a protein you use the following parameters in the mdp file. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per n pull_k1 = 1000 ; kJ mol^-1 nm^- How should I alter this to pull the molecules together along the z axis? I would've thought the following but I'm not too sure pull= umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_rate1 = -0.01 pull_k1 = 1000 Obviously I have to play with the values, but it is the sign that I'm interested in. Have you tried it? I think it should do what you want. Otherwise, it is probably easier to use pull_geometry = direction and specify the actual vector along which to pull. The tutorial is only really useful from a conceptual standpoint, and for a system in which pulling is applied in only one direction to cause a positive displacement. -Justin Many Thanks Gavin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Hi Justin Thanks. If I use the pull_geometry = direction I would go for the following jus t to pull the molecules together in the z direction. pull= umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 pull_k1 = 1000 Does this seem reasonable? Also in the pull_rate what is meant by the 'rate of change of the reference position'? (Is it the position of the reference group, if so what if I don't want it to change?) Cheers Gavin -- 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
Gavin Melaugh wrote: Hi Justin Thanks. If I use the pull_geometry = direction I would go for the following jus t to pull the molecules together in the z direction. pull= umbrella pull_geometry = direction pull_start = yes pull_ngroups = 1 pull_group0 = cage_1 pull_group1 = cage_2 pull_vec1 = 0.0 0.0 -1.0 pull_rate1 = 0.01 pull_k1 = 1000 Does this seem reasonable? Also in the pull_rate what is meant by the Probably. Try it. 'rate of change of the reference position'? (Is it the position of the reference group, if so what if I don't want it to change?) It is the rate of change of the reference position, which is the position at the outset of the simulation. Your objective is to pull your two species together, right? I don't see why you wouldn't want it to change. You're not changing anything about pull_group0 (your reference group), since you aren't setting pull_rate0. Everything is applied to pull_group1 (hence _rate1, _k1, etc). -Justin Cheers Gavin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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, 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 5.04012 -1.03421 95.4000 5.03944 -1.05723 95.6000 5.03981 -1.00803 95.8000 5.04072 -1.01506 96. 5.04055 -0.980655 $ tail
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 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
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_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
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_init10, 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 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_init10, 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, 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
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 AND NpT ensemble
Hi, I would use v-rescale and Berendsen pressure coupling. Although Berendsen pressure coupling, strictly speaking, does not give the correct ensemble, in practice it produces negligible artifacts, unless you are looking at pressure/volume fluctuations. Berk To: gmx-users@gromacs.org Date: Thu, 27 Aug 2009 07:20:00 -0400 From: gigita...@aol.fr Subject: [gmx-users] PULL CODE AND NpT ensemble Hi all, I would like to use pull code to evaluate the free energy of pulling system1 from system2. Free energy calculation should be done for NpT ensemble. All tutorials found for calculating free energy used 1) berensen for T and P coupling or 2) berensen for T coupling AND Parrinelo for P coupling or 3)Vrescale for T and no P coupling I am a bit lost in which one should lead to real ensemble. Is any one could help? Regards, geraldine, phD _ 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 AND NpT ensemble
Hi Berk, Thanks for your answer. I just want to be sure that the procedure is correct. No I do not look at the pressure/volume fluctutation. But I do want to make a clever choice of the ensemble so that no significant extra artifact are generated, since the number of contraint to be calculated is not negligible. I previously used no P coupling and I was wondering is that feature could explain that the average force plot is not smooth function. Other criteria such as Cut-off value for LJ and coulomb may also be checked out? Geraldine -E-mail d'origine- De : Berk Hess g...@hotmail.com A : Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Jeudi, 27 Août 2009 13:45 Sujet : RE: [gmx-users] PULL CODE AND NpT ensemble Hi, I would use v-rescale and Berendsen pressure coupling. Although Berendsen pressure coupling, strictly speaking, does not give the correct ensemble, in practice it produces negligible artifacts, unless you are looking at pressure/volume fluctuations. Berk To: gmx-users@gromacs.org Date: Thu, 27 Aug 2009 07:20:00 -0400 From: gigita...@aol.fr Subject: [gmx-users] PULL CODE AND NpT ensemble Hi all, I would like to use pull code to evaluate the free energy of pulling system1 from system2. Free energy calculation should be done for NpT ensemble. All tutorials found for calculating free energy used 1) berensen for T and P coupling or 2) berensen for T coupling AND Parrinelo for P coupling or 3)Vrescale for T and no P coupling I am a bit lost in which one should lead to real ensemble. Is any one could help? Regards, geraldine, phD Express yourself instantly with MSN Messenger! MSN Messenger= ___ 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 ___ 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: Re : [gmx-users] PULL CODE AND NpT ensemble
Hi, There are no settings that matter in particular for pulling compared to a normal simulation. All the settings that matter normally matter here as well. NVT pulling should give nearly identical results no NPT, as long as you set the volume correctly. Berk To: gmx-users@gromacs.org Subject: Re : [gmx-users] PULL CODE AND NpT ensemble Date: Thu, 27 Aug 2009 08:03:56 -0400 From: gigita...@aol.fr Hi Berk, Thanks for your answer. I just want to be sure that the procedure is correct. No I do not look at the pressure/volume fluctutation. But I do want to make a clever choice of the ensemble so that no significant extra artifact are generated, since the number of contraint to be calculated is not negligible. I previously used no P coupling and I was wondering is that feature could explain that the average force plot is not smooth function. Other criteria such as Cut-off value for LJ and coulomb may also be checked out? Geraldine -E-mail d'origine- De : Berk Hess g...@hotmail.com A : Discussion list for GROMACS users gmx-users@gromacs.org Envoyé le : Jeudi, 27 Août 2009 13:45 Sujet : RE: [gmx-users] PULL CODE AND NpT ensemble Hi, I would use v-rescale and Berendsen pressure coupling. Although Berendsen pressure coupling, strictly speaking, does not give the correct ensemble, in practice it produces negligible artifacts, unless you are looking at pressure/volume fluctuations. Berk To: gmx-users@gromacs.org Date: Thu, 27 Aug 2009 07:20:00 -040 0 From: gigita...@aol.fr Subject: [gmx-users] PULL CODE AND NpT ensemble Hi all, I would like to use pull code to evaluate the free energy of pulling system1 from system2. Free energy calculation should be done for NpT ensemble. All tutorials found for calculating free energy used 1) berensen for T and P coupling or 2) berensen for T coupling AND Parrinelo for P coupling or 3)Vrescale for T and no P coupling I am a bit lost in which one should lead to real ensemble. Is any one could help? Regards, geraldine, phD Express yourself instantly with MSN Messenger! MSN Messenger= ___ 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 in terface 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 problem
Hi, First, please switch to 4.0.5, I have put several fixes in the pull code in the 4.0 minor releases. You did not specify pull_init1, nor pull_start, this means you start pulling at a distance of 0, which means the center of the bilayer. Setting pull_start = yes should fix your problem. Berk Date: Thu, 6 Aug 2009 10:49:26 +0800 From: djpit...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] pull code problem Hi, all: I tried to pull a specific DPPC, say, r3, out of a pre-equilibrated bilayer into the water along the positive z axis. For the pull code parameters, I used: pull = umbrella pull_geometry= distance pull_vec1 = 0. 0. 1. pull_dim= N N Y pull_nstxout = 1000 pull_group0 = bilayer pull_group1 = r3_P pull_k1 = 500 pull_rate1 = 0.001;nm/ps integrator = md dt = 0.002 ;ps nsteps = 100 nstcomm = 1 comm_grps = DPP SOL nstxtcout = 100 nstlist = 10 ns_type = grid pbc = xyz rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 ewald_rtol = 1e-5 optimize_fft= yes tcoupl = Berendsen tau_t = 0.10.1 tc_grps = DPPSOL ref_t = 323323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 gen_vel = no gen_temp= 323 gen_seed= 173529 constraints = all-bonds constraint_algorithm= LINCS lincs_order = 4 r3_P corresponds to an index file that contains the phophorus group of r3, and bilayer corresponds to an index file that contains all the lipids except r3. I'm using GROMACS 4.0.3, but when I looked at the trajectory in VMD, the position of r3 is hardly moved. So what's the right way to pull this specific lipid into the water slab? Thanks. dj _ 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 problem
Hi, Do you have another line with pull = somewhere in your mdp file? PS You should switch to Gromacs 4.0.4, since it contains several small bug fixes for the pull code. Berk Date: Mon, 11 May 2009 12:38:35 +0300 From: neamtuand...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] pull code problem hello, I am trying to do a pulling simulation with gromacs 4.0.2 I added the following lines to the .mdp input file for grompp: ... pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 2 pull_group0= Protein pull_group1= CA2+1 pull_rate1 = 0.3 pull_group2= CA2+2 pull_rate2 = 0.3 . when I run grompp -f production_prm.mdp ...etc. it does not recognize the keywords for pulling: Ignoring obsolete mdp entry 'title' Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to ./#neutr_RCK_Mthk_solv.04.mdout.mdp.6# WARNING 1 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_geometry' in parameter file WARNING 2 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_dim' in parameter file WARNING 3 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_nstxout' in parameter file WARNING 4 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_nstfout' in parameter file WARNING 5 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_ngroups' in parameter file WARNING 6 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_group0' in parameter file WARNING 7 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_group1' in parameter file WARNING 8 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_rate1' in parameter file WARNING 9 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_group2' in parameter file WARNING 10 [file production_prm.mdp, line unknown]: Unknown or double left-hand 'pull_rate2' in parameter file ... It appears that grompp doesnot recognize any of these keywords... Does anybody can help? Thank you Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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 problem
Hi, Maybe there is an older grompp in your path. Type grompp -h to see which version you are using. And: which grompp to see where it comes from. Berk Date: Mon, 11 May 2009 13:03:07 +0300 From: neamtuand...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] pull code problem Hi Berk, thank you for the reply here is my mdp file: ; ; User aneamtu ; Joi, 7 mai - 2009 ; Input file ; title = Production_runs ;define = -DPOSRES -DPOSRES_CA2+_IONS ;constraints = all-bonds integrator = md dt = 0.001 nsteps = 5 nstcomm= 1 nstxout= 1000 nstvout= 1000 nstfout= 1000 nstlog = 500 nstxtcout = 50 xtc_grps = Protein_ions nstenergy = 100 nstlist= 10 ns_type= grid coulombtype= PME rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 optimize_fft = yes Tcoupl = v-rescale tc-grps = Protein SOL ions tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 energygrps = Protein SOL CA2+ NA+ CL- Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility= 4.5e-5 ref_p = 1.0 gen_vel= no gen_temp = 310.0 gen_seed = 173529 pull = constraint pull_geometry = distance pull_dim = Y Y Y pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 2 pull_group0= Protein pull_group1= CA2+1 pull_rate1 = 0.3 pull_group2= CA2+2 pull_rate2 = 0.3 I do not understand what I do wrong.. Should I use a -pi pull.ppa file like in gromacs 3.x ? Andrei ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.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 absolute reference artifacts
Hi, I have no clue why you would want to fix the peptide in the middle of the box. But what you want seems to be more like com removal for the peptide only with the comm options. The pull code will do approximately what you want, but with pressure coupling there is the problem that your peptide will stay fixed in space, while the rest of the system has to scale around it. In general there are problems with absolute reference pulling, because you just fix the location of the pull group, whereas the rest of the system can freely move, thus the net effect is zero, except for lots of nasty artifacts when you change the pull position too fast. Berk Date: Thu, 16 Apr 2009 10:27:04 -0400 From: chris.ne...@utoronto.ca To: gmx-users@gromacs.org Subject: [gmx-users] pull code absolute reference artifacts Hello, I have a question about the following grompp 4.0.4 warning: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. While I do realize that this is an excellent error message containing lots of information, I am still unclear about how to proceed. Why does my system not have an absolute reference? Is it because I have pbc and center of mass motion removal? Exactly what types of artifacts are expected? Is there a simple solution? I am trying to hold my peptide in the center of a water box. I realize that there is no center and everything in pbc, but I need to do it nevertheless. Here are my .mdp options: pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_ngroups= 1 ;pull_group0 = pull_group1 = peptide_A pull_k1 = 500 pull_init1 = 0.00 nsteps = 25 ; REMOVE_FOR_EM tinit = 49000 ; REMOVE_FOR_EM dt = 0.004 ; REMOVE_FOR_EM nstxout = 25 ; REMOVE_FOR_EM nstvout = 25 ; REMOVE_FOR_EM nstfout = 25 ; REMOVE_FOR_EM nstenergy = 25000 ; REMOVE_FOR_EM nstxtcout = 25000 ; REMOVE_FOR_EM nstlog = 25; REMOVE_FOR_EM gen_vel = no unconstrained-start = yes integrator = sd gen_seed= -1 comm_mode = linear nstcomm = 1 comm_grps = System nstlist = 5 ns_type = grid pbc = xyz coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 DispCorr= EnerPres Pcoupl = Berendsen ; REMOVE_FOR_EM pcoupltype = isotropic ; REMOVE_FOR_EM compressibility = 4.5e-5 ; REMOVE_FOR_EM ref_p = 1. ; REMOVE_FOR_EM tau_p = 4.0; REMOVE_FOR_EM tc_grps = System ; REMOVE_FOR_EM tau_t = 1.0; REMOVE_FOR_EM ld_seed = -1 ; REMOVE_FOR_EM ref_t = 300. ; REMOVE_FOR_EM gen_temp= 300. ; REMOVE_FOR_EM constraints = all-bonds ; REMOVE_FOR_EM constraint_algorithm= lincs ; REMOVE_FOR_EM lincs-iter = 1 ; REMOVE_FOR_EM lincs-order = 6 ; REMOVE_FOR_EM ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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 absolute reference artifacts
Hi Justin: 1) EXTREMELY IMPORTANT: I already know of 1 person, but is anyone alergic to either Iodine or Chlorine? No, I am not alergic to those compounds. The only thing that I am alergic is Penicillin and Ampicilin. 2) Any other medical problems? No 3) An Emergency contact person. Fernando Babilonia. Telf: 646 752 6557 4) What food are you planning on bringing? If anyone is planning on bringing food that needs to be heated, cooked, or boiled i need to re-calculate how much fuel we need for the stove incase the rain prevents us from lighting a fire. I am planning to take fast easy food like tuna or sandwiches. The only thing that i am planning to use heat is to boil water for instant tea and also I planning to have some hotdogs at dinner. -Rodney ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 using two reaction coordinates??
Hi Rodney, the other alternative is to define the springs in your topology file. You first need to merge your groups (is part of different molecules) and run the different combination you need by defining them by hand; you can easily write a awk script to generate the different topologies you need. Then you can use a 2D wham to combine the different histograms you've obtained and get your 2D PMF. XAvier. On Mar 16, 2009, at 8:28 PM, rvers...@ccny.cuny.edu rvers...@ccny.cuny.edu wrote: Hello everybody: I am trying to perform some PMF calculations using the pull code with a spring (umbrella sampling) but using two reaction coordinates (E1 and E2) between four different groups (r1,r2,r3 and r4). All the examples and tutorials that I found so far on the web, only mention PMF calculations for one reaction coordinate (E1) between two different groups (r1 and r2). Is it possible to perform the calculations using two reaction coordinates at the same time or should i do two different individual calculations or there is something more that i should do to achieve it? I will appreciate any help. -Rodney ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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, lambda, and soft core availability
This seems to be a good reference for soft-core interactions. BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys Lett (1994) vol. 222 pp. 529-539 On Thu, Feb 12, 2009 at 1:33 PM, chris.ne...@utoronto.ca wrote: Does anybody know of a good paper that describes the underlying equations that define soft core? Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
avinash kumar wrote: Hello all, does anybody possess a sample of pull.pdo data file for pull codes. The pull.pdo file is output, are you sure that's what you want, or do you want a pull.ppa input file? Either way, enter pull.pdo or pull.ppa into the Search page for the archive and you will get tons of hits. -Justin -- Justin A. Lemkul Graduate Research Assistant 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://www.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 problems
Hi, You don't indicate which xvg file was 0, I guess pullf.xvg. Could it be that you did not specify a force constant, meaning fc=0? Berk From: gene...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Jan 2009 14:26:47 +0300 Subject: [gmx-users] Pull Code problems Hello, I am trying to run a pulling simulation with gromacs 4.0.2. I have appended the following pull code to the mdp file: ;---PULL CODE - pull = umbrella pull_geometry = direction pull_group0 = r_500 pull_group1 = r_535 pull_vec1 = -1.306 1.355 -0.319 Where r_500 is the group I am expecting to be pulled, r_535 - the reference (the acid that is in fact in contact with r_500) I have left all remaining parameters with default values. The problem is that NOTHING HAPPENED! XVG file had 0. throughout simulation indicating that distance between pull group and reference group was 0! 1/ What did I do wrong? 2/ Is there any pull code tutorial for gromacs 4 (not previous version)? Thank you! SDA ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.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 problems
OK, I did some homework and now I`m up to this: ;---PULL CODE - pull= umbrella pull_geometry = direction pull_group0 = r_500 pull_group1 = r_535 pull_vec1 = -1.306 1.355 -0.319 pull_k1 = 1000 pull_rate1 = 0.5 ; nm/ps Extreme parameters for extreme pulling Now I have two output files - pullx.xvg (-px option of mdrun) and pullf.xvg (-pf option). pullx : @title Pull COM @xaxis label Time (ps) @yaxis label Position (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 X @ s1 legend 0 Y @ s2 legend 0 Z @ s3 legend 1 dX @ s4 legend 1 dY @ s5 legend 1 dZ 0.003.8995935.8163683.246447 -0.285972 -0.132647 -0.183023 0.043.9011635.8121323.238992 -0.292108 -0.141616 -0.180796 0.083.9025055.8062123.240236 -0.314770 -0.143951 -0.186194 0.123.9053655.7979383.242384 -0.336802 -0.142276 -0.197704 0.163.9088995.7948123.230687 -0.342824 -0.160593 -0.178745 0.203.9101085.7975643.220754 -0.340151 -0.161146 -0.152076 Am I correct about XYZ being position of the spring and dx dy dz - group0-group1 distances? pullf : @title Pull force @xaxis label Time (ps) @yaxis label Force (kJ/mol/nm) @TYPE xy 0.00-132.088161 0.004000-128.605515 0.008000-125.008520 0.012000-121.568624 0.016000-118.475655 0.02-115.844403 0.024000-113.735184 0.028000-112.165522 0.032000-111.066433 . ... 1.232000409.573773 1.236000412.738957 1.24415.736038 1.244000418.446270 1.248000420.781766 1.252000422.747570 1.256000424.505472 1.26426.348269 1.264000428.568933 1.268000431.301610 1.272000434.467394 Why does it start with negative values? Should I use negative value for pull_k1 (force constant)? Thank you for your answers, I appreciate your time. SDA On Tue, 2009-01-13 at 12:41 +0100, Berk Hess wrote: Hi, You don't indicate which xvg file was 0, I guess pullf.xvg. Could it be that you did not specify a force constant, meaning fc=0? Berk From: gene...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Jan 2009 14:26:47 +0300 Subject: [gmx-users] Pull Code problems Hello, I am trying to run a pulling simulation with gromacs 4.0.2. I have appended the following pull code to the mdp file: ;---PULL CODE - pull = umbrella pull_geometry = direction pull_group0 = r_500 pull_group1 = r_535 pull_vec1 = -1.306 1.355 -0.319 Where r_500 is the group I am expecting to be pulled, r_535 - the reference (the acid that is in fact in contact with r_500) I have left all remaining parameters with default values. The problem is that NOTHING HAPPENED! XVG file had 0. throughout simulation indicating that distance between pull group and reference group was 0! 1/ What did I do wrong? 2/ Is there any pull code tutorial for gromacs 4 (not previous version)? Thank you! SDA ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 __ What can you do with the new Windows Live? Find out ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 problems
Hi, pullx.xvg has the coordinates of group 0 and the distances of the other groups to group 0. pullf.xvg has the force of the umbrella potential which works along the direction vector you gave, this can be positive or negative depending on the direction. Berk Subject: RE: [gmx-users] Pull Code problems From: gene...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Jan 2009 18:02:47 +0300 OK, I did some homework and now I`m up to this: ;---PULL CODE - pull= umbrella pull_geometry = direction pull_group0 = r_500 pull_group1 = r_535 pull_vec1 = -1.306 1.355 -0.319 pull_k1 = 1000 pull_rate1 = 0.5 ; nm/ps Extreme parameters for extreme pulling Now I have two output files - pullx.xvg (-px option of mdrun) and pullf.xvg (-pf option). pullx : @title Pull COM @xaxis label Time (ps) @yaxis label Position (nm) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 X @ s1 legend 0 Y @ s2 legend 0 Z @ s3 legend 1 dX @ s4 legend 1 dY @ s5 legend 1 dZ 0.003.8995935.8163683.246447 -0.285972 -0.132647 -0.183023 0.043.9011635.8121323.238992 -0.292108 -0.141616 -0.180796 0.083.9025055.8062123.240236 -0.314770 -0.143951 -0.186194 0.123.9053655.7979383.242384 -0.336802 -0.142276 -0.197704 0.163.9088995.7948123.230687 -0.342824 -0.160593 -0.178745 0.203.9101085.7975643.220754 -0.340151 -0.161146 -0.152076 Am I correct about XYZ being position of the spring and dx dy dz - group0-group1 distances? pullf : @title Pull force @xaxis label Time (ps) @yaxis label Force (kJ/mol/nm) @TYPE xy 0.00-132.088161 0.004000-128.605515 0.008000-125.008520 0.012000-121.568624 0.016000-118.475655 0.02-115.844403 0.024000-113.735184 0.028000-112.165522 0.032000-111.066433 . ... 1.232000409.573773 1.236000412.738957 1.24415.736038 1.244000418.446270 1.248000420.781766 1.252000422.747570 1.256000424.505472 1.26426.348269 1.264000428.568933 1.268000431.301610 1.272000434.467394 Why does it start with negative values? Should I use negative value for pull_k1 (force constant)? Thank you for your answers, I appreciate your time. SDA On Tue, 2009-01-13 at 12:41 +0100, Berk Hess wrote: Hi, You don't indicate which xvg file was 0, I guess pullf.xvg. Could it be that you did not specify a force constant, meaning fc=0? Berk From: gene...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Jan 2009 14:26:47 +0300 Subject: [gmx-users] Pull Code problems Hello, I am trying to run a pulling simulation with gromacs 4.0.2. I have appended the following pull code to the mdp file: ;---PULL CODE - pull = umbrella pull_geometry = direction pull_group0 = r_500 pull_group1 = r_535 pull_vec1 = -1.306 1.355 -0.319 Where r_500 is the group I am expecting to be pulled, r_535 - the reference (the acid that is in fact in contact with r_500) I have left all remaining parameters with default values. The problem is that NOTHING HAPPENED! XVG file had 0. throughout simulation indicating that distance between pull group and reference group was 0! 1/ What did I do wrong? 2/ Is there any pull code tutorial for gromacs 4 (not previous version)? Thank you! SDA ___ gmx-users mailing list gmx-users@gromacs.org http://www.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 __ What can you do with the new Windows Live? Find out ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Pull Code problems
OK, I have a new problem. I`ve started the simulation with the following pull parameters ;---PULL CODE - pull--=- umbrella pull_geometry-= direction pull_group0--= r_500 pull_group1---= r_535 pull_vec1-= -1.306 1.355 -0.319 pull_k1--= 1000 pull_rate1= 1 ; nm/ps = 1 A/ns With such extreme pulling velocities I had my system teared apart in 100 ps - that is OK I suggest. The problem is that pull group (pull_group1) and reference group (pull_group0) were both pulled in opposite directions - pull_vec1 and -(pull_vec1)?! 1/ In my best understanding the reference group is the one that stays intact to track the movement of the group that is being pulled - pull group. Then how could this happen in my system? What should I do to pull only the pull_group1? 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new name for AFM in gromacs 4? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 problems
Hi, The pull option acts between COM's. Both COM's will move. If not, you would have a net force on the COM of the whole system. The AFM option is no longer there. I never understood what the difference between Umbrella and AFM was. But Umbrella (as well as constraint) should be able to do all things that were possible before (and more). Berk Subject: Re: [gmx-users] Pull Code problems From: gene...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Jan 2009 18:44:36 +0300 OK, I have a new problem. I`ve started the simulation with the following pull parameters ;---PULL CODE - pull--=- umbrella pull_geometry-= direction pull_group0--= r_500 pull_group1---= r_535 pull_vec1-= -1.306 1.355 -0.319 pull_k1--= 1000 pull_rate1= 1 ; nm/ps = 1 A/ns With such extreme pulling velocities I had my system teared apart in 100 ps - that is OK I suggest. The problem is that pull group (pull_group1) and reference group (pull_group0) were both pulled in opposite directions - pull_vec1 and -(pull_vec1)?! 1/ In my best understanding the reference group is the one that stays intact to track the movement of the group that is being pulled - pull group. Then how could this happen in my system? What should I do to pull only the pull_group1? 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new name for AFM in gromacs 4? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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 problems
OK, finally I try to simplify my question by revealing my final aim. I have a group that I want to pull out of my protein. I want only one group to be pulled out in one direction. How could I do that? SDA P.S. In my understanding to do that I should leave reference group blank and specify pull group only: pull_group0= pull_group1=r_535 In this case grompp calculates initial distance from (0,0,0) to pull group and sets the initial force to a very high value (distance*force_constant) instead of 0. To correct this and to make the initial pull rate = 0 I should set pull group to the center of coordinates or set the initial position of the pull spring to the position of the pull group. How should I do that? On Tue, 2009-01-13 at 16:55 +0100, Berk Hess wrote: Hi, The pull option acts between COM's. Both COM's will move. If not, you would have a net force on the COM of the whole system. The AFM option is no longer there. I never understood what the difference between Umbrella and AFM was. But Umbrella (as well as constraint) should be able to do all things that were possible before (and more). Berk Subject: Re: [gmx-users] Pull Code problems From: gene...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Jan 2009 18:44:36 +0300 OK, I have a new problem. I`ve started the simulation with the following pull parameters ;---PULL CODE - pull--=- umbrella pull_geometry-= direction pull_group0--= r_500 pull_group1---= r_535 pull_vec1-= -1.306 1.355 -0.319 pull_k1--= 1000 pull_rate1= 1 ; nm/ps = 1 A/ns With such extreme pulling velocities I had my system teared apart in 100 ps - that is OK I suggest. The problem is that pull group (pull_group1) and reference group (pull_group0) were both pulled in opposite directions - pull_vec1 and -(pull_vec1)?! 1/ In my best understanding the reference group is the one that stays intact to track the movement of the group that is being pulled - pull group. Then how could this happen in my system? What should I do to pull only the pull_group1? 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new name for AFM in gromacs 4? Thanks. ___ gmx-users mailing list gmx-users@gromacs.org http://www.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! MSN Messenger ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 problems
Hi, If you pull without a reference, you will be doing nothing in the limit of slow pulling. For fast pulling you will be doing something. pull_start=yes pull_init1=0 will initialize set pull_init to the initial distance. Berk Subject: RE: [gmx-users] Pull Code problems From: gene...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Jan 2009 19:59:38 +0300 OK, finally I try to simplify my question by revealing my final aim. I have a group that I want to pull out of my protein. I want only one group to be pulled out in one direction. How could I do that? SDA P.S. In my understanding to do that I should leave reference group blank and specify pull group only: pull_group0= pull_group1=r_535 In this case grompp calculates initial distance from (0,0,0) to pull group and sets the initial force to a very high value (distance*force_constant) instead of 0. To correct this and to make the initial pull rate = 0 I should set pull group to the center of coordinates or set the initial position of the pull spring to the position of the pull group. How should I do that? On Tue, 2009-01-13 at 16:55 +0100, Berk Hess wrote: Hi, The pull option acts between COM's. Both COM's will move. If not, you would have a net force on the COM of the whole system. The AFM option is no longer there. I never understood what the difference between Umbrella and AFM was. But Umbrella (as well as constraint) should be able to do all things that were possible before (and more). Berk Subject: Re: [gmx-users] Pull Code problems From: gene...@gmail.com To: gmx-users@gromacs.org Date: Tue, 13 Jan 2009 18:44:36 +0300 OK, I have a new problem. I`ve started the simulation with the following pull parameters ;---PULL CODE - pull--=- umbrella pull_geometry-= direction pull_group0--= r_500 pull_group1---= r_535 pull_vec1-= -1.306 1.355 -0.319 pull_k1--= 1000 pull_rate1= 1 ; nm/ps = 1 A/ns With such extreme pulling velocities I had my system teared apart in 100 ps - that is OK I suggest. The problem is that pull group (pull_group1) and reference group (pull_group0) were both pulled in opposite directions - pull_vec1 and -(pull_vec1)?! 1/ In my best understanding the reference group is the one that stays intact to track the movement of the group that is being pulled - pull group. Then how could this happen in my system? What should I do to pull only the pull_group1? 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new name for AFM in gromacs 4? Thanks. ___ gmx-users mailing list gmx-users@gromacs.org http://www.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! MSN Messenger ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.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 runtype start
I searched the on line document for runtype and got nothing. But in the Manual in chapter 6 there is an overveiw of the pull code options and one of the options listed is the starting structures and it says the keyword for runtype to use for this is start. On 10/19/07 6:55 PM, Mark Abraham [EMAIL PROTECTED] wrote: dtmirij wrote: Hello everyone, I just want to clarify if the runtype start option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. Did you try searching the manual for runtype? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code with runtype start
dtmirij wrote: I searched the on line document for runtype and got nothing. But in the Manual in chapter 6 there is an overveiw of the pull code options and one of the options listed is the starting structures and it says the keyword for runtype to use for this is start. http://www.gromacs.org/content/view/27/42/ Neither starting structures nor start (in this context) are mentioned in the 3.3.1 manual?? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code with runtype start
Mark, I just checked and it seems I was consulting a manual for an older version than 3.3.1! I guess it was taken out in 3.3.1 Sorry for not being more careful. Thank you. -Dina On 10/20/07 4:16 PM, Mark Abraham [EMAIL PROTECTED] wrote: dtmirij wrote: I searched the on line document for runtype and got nothing. But in the Manual in chapter 6 there is an overveiw of the pull code options and one of the options listed is the starting structures and it says the keyword for runtype to use for this is start. http://www.gromacs.org/content/view/27/42/ Neither starting structures nor start (in this context) are mentioned in the 3.3.1 manual?? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code with runtype start
dtmirij wrote: Hello everyone, I just want to clarify if the runtype start option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. Did you try searching the manual for runtype? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code methods?
I'm no umbrella user, but as far as I know, you have to set different parameters, according to the manual. These may be similar to the AFM parameters, but still, in the config file, they are separated. Sure, you don't define a pull rate for Umbrella, because you build, as you said, discrete systems, where you put the umbrella potential onto one group along a reaction coordinate. It's clear that, depending on your system, you have to build N systems where your ligand is moved away from the protein along the reaction coordinate. Now, I'm curious about you asking about afm_init again...so you are finished with the umbrella business and want to do AFM now? The sentence, in fact, is very clear. You can break down the statement to: Calculate the resulting vector from the difference of two other vectors Therefore you have to find two vectors. One should be the COM of your reference group (you could also choose a single atom there...Just makes no sense to me) and one is either the COM of your ligand or, better, one single atom of your ligand, where the spring(AFM-tip) is attached to... I think, this has been discussed in the mailing list more than once... Maybe you should intensively search the archive for such things... regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Hi Maik, Thank you for the answer. I still have some questions. I still didn't get the umberalla sampling method. It seems to me AFM and umberalla are the same except that in umberalla we dont define a Pull rate. Looking at the literature, people have been using umberalla method with discrete simulations. i.e. 21 simulation windows. I kind of get the idea that you will have to manually set up the the 21 discrete simulations to get the final separated ligand-protein for the umberalla method? correct me if I am wrong. The other question I had is about init-afm position option. it says in the manual: afm init1 = Vector describing the initial position of the spring relative to the reference group. To start a simulation with zero initial force on the pulled group, the initial position should be set to the position of the pulled group relative to the reference group. This sentence is very unclear to me. how do u calculated the poition of the pulled group relative to the referene. Is is by calculating the Center of mass of the pulled group or by calculating the center of mass of the the whole system (pulled group + reference)? Thank you, Belquis Hi You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF you want to calculate (runtype=afm,umbrella). Depending on this choice it's very likely that the afm_rate is simply ignored for umbrella, no? The force constant is mimicking the stiffness of the spring. You want to obey the stiff spring approximation (which still does NOT mean, you should use a rod ;) ) and therefore shouldn't choose the fc of the spring to small. I usually use a force constant of 500 kJ/mol*nm^2. It actually DOES make sense, to choose a fc comparable to the experiments, you want to compare your sim with, IF you want to compare :) Hope that helps Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling (contraint_rate, AFM_rate), however, for umberalla, there is only two options, a foce constant and position to be specified! my question is: how is the pulling controlled in umberalla sampling option? 2) if I want to do an AFM pulling...what is a reasonalble force constant to use? it seems people are using different K ranging from 10 to 1000's? thank u Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] Pull code methods?
Hi Maik, Thank you for the answer. I still have some questions. I still didn't get the umberalla sampling method. It seems to me AFM and umberalla are the same except that in umberalla we dont define a Pull rate. Looking at the literature, people have been using umberalla method with discrete simulations. i.e. 21 simulation windows. I kind of get the idea that you will have to manually set up the the 21 discrete simulations to get the final separated ligand-protein for the umberalla method? correct me if I am wrong. The other question I had is about init-afm position option. it says in the manual: afm init1 = Vector describing the initial position of the spring relative to the reference group. To start a simulation with zero initial force on the pulled group, the initial position should be set to the position of the pulled group relative to the reference group. This sentence is very unclear to me. how do u calculated the poition of the pulled group relative to the referene. Is is by calculating the Center of mass of the pulled group or by calculating the center of mass of the the whole system (pulled group + reference)? Thank you, Belquis Hi You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF you want to calculate (runtype=afm,umbrella). Depending on this choice it's very likely that the afm_rate is simply ignored for umbrella, no? The force constant is mimicking the stiffness of the spring. You want to obey the stiff spring approximation (which still does NOT mean, you should use a rod ;) ) and therefore shouldn't choose the fc of the spring to small. I usually use a force constant of 500 kJ/mol*nm^2. It actually DOES make sense, to choose a fc comparable to the experiments, you want to compare your sim with, IF you want to compare :) Hope that helps Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling (contraint_rate, AFM_rate), however, for umberalla, there is only two options, a foce constant and position to be specified! my question is: how is the pulling controlled in umberalla sampling option? 2) if I want to do an AFM pulling...what is a reasonalble force constant to use? it seems people are using different K ranging from 10 to 1000's? thank u Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code methods?
Hi You have to tell GROMACS in the parameters-file (.ppa) which kind of PMF you want to calculate (runtype=afm,umbrella). Depending on this choice it's very likely that the afm_rate is simply ignored for umbrella, no? The force constant is mimicking the stiffness of the spring. You want to obey the stiff spring approximation (which still does NOT mean, you should use a rod ;) ) and therefore shouldn't choose the fc of the spring to small. I usually use a force constant of 500 kJ/mol*nm^2. It actually DOES make sense, to choose a fc comparable to the experiments, you want to compare your sim with, IF you want to compare :) Hope that helps Regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ [EMAIL PROTECTED] wrote: Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling (contraint_rate, AFM_rate), however, for umberalla, there is only two options, a foce constant and position to be specified! my question is: how is the pulling controlled in umberalla sampling option? 2) if I want to do an AFM pulling...what is a reasonalble force constant to use? it seems people are using different K ranging from 10 to 1000's? thank u Belquis ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code with shuffle/sort options
Thank you Chris for providing recognition of this issue. -Steve Chris Neale wrote: I have encountered noticeable differences while using the pull code with the -shuffle -sort options in parallel, as opposed to running in serial or in parallel without the options. Using -shuffle -sort, the dynamics of the molecule of interest appears to be unaffected by the pulling potential. Without the options, the molecule can be seen to be correctly pulled in the desired direction. I'm using version 3.3.1, and this problem is present in both single and double precision versions. I recall that this is also the case for position restraints and a shuffled or sorted run. I believe that this is a known issue and that there is no solution. However, I can't remember where I read that I didn't find it either with a quick search of the mailing list and the manual fo things like posre shuffle or restraint shuffle ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
