Re: [gmx-users] Pressure Fluctuations
On 16/03/11, Kavyashree M wrote: > Dear users, > > Upon was trying to simulate an npt ensemble (protein in water), > pressure was coupled using parinello rahman system with tau_p = 2, > tau_t = 1; compressibility 4.5e-5, type = isotropic. > > (cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9; > > rcoulomb = 1.2; rlist = 1.2). > > No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3, 3.5), the pressure > fluctuations are very drastic. I have gone through the mailing list regarding > this issue but could not come to any conclusion. > > > Any suggestions are helpfull. > > This is one of the statistics for pressure fluctuations. > > Statistics over 51 steps [ 0. through 1000. ps ], 1 data sets > All statistics are over 11 points > > > Energy Average Err.Est. RMSD Tot-Drift > --- > Pressure 5.77629 0.99 398.013 -5.34218 (bar) > Looks very normal. See http://www.gromacs.org/Documentation/FAQs number 3 Mark -- 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] Re: g_hbond output
@ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 : 5 3 2 Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 if the $3 means pairs. I tried pymol, and on the last frame, there were 4 hydrogen bonds, between 7 residues. it's different from here 3 2 Thanks and sorry for last email without my realization it sent. lina -- 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] g_hbond output
@ legend length 2 @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 : -- 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] Replacing a residue and continuing a simulation run
Hi :) I'd say that if the changes are small you should be able to get away with it. You might want to start off the second part of the run with a smaller time step to relax, though. If the change is from TRP to TRP*, you only need to have a modified topology, without touching the coordinates. You do need to set up a new .tpr file from the the .trr and the modified topology. Hope it helps, Tsjerk On Tue, Mar 15, 2011 at 10:11 PM, Justin A. Lemkul wrote: > > > J. Nathan Scott wrote: >> >> Hello all, >> >> I was wondering, is it possible to replace a residue and then continue >> a simulation using the new parameters/geometry of the new residue? The >> reason I ask is that I am interested in performing simulations of >> proteins with tryptophan in its excited state following a lengthy >> equilibration with TRP in its ground state. I already have reliable >> excited state atomic charges for the TRP atoms, and I suppose that I >> will need to change at least some bonded terms to account for the >> altered geometry of the excited state. >> >> I am still in the middle of reading the information that is out there >> regarding parameterizing new molecules (since I'm using the CHARMM FF, >> I've been starting to follow Alexander MacKerell's protocols), but I'm >> still not quite sure as to how one would practically do this residue >> replacement in the context of a Gromacs run. Will I need to manually >> edit my .top file, or is there perhaps another way to update the >> topology file with the new residue following the ground state >> equilibration? How about coordinates, will I need to transform the TRP >> coordinates to the excited state geometry by hand? >> > > You would have to hack the topology. Coordinates are another matter. If > you start making ad hoc changes, then what's the point of a continuation? > Presumably, if you've designed the residue's topology correctly (including > both bonded and nonbonded parameters), then the residue will adopt the > correct geometry on its own. > > The complication comes with bonded interactions. Are you using constraints? > If so, then changing bond lengths will cause the constraints to fail at > step 0 (or very soon thereafter) and the simulation will crash. You can get > around this by setting "continuation = no" in the .mdp file, but again I > wonder what the value of the continuation is. You'd almost certainly have > to forgo the use of .cpt files, supplying instead your .trr and .edr files > to preserve as much of the previous ensemble as possible. Even if you're > not using constraints, the simulation may still fail if you're suddenly > changing bond lengths, angles, etc by anything more than a very small > amount. > >> Perhaps the most important question: is there a better way to do the >> sort of residue replacement I'm contemplating, or is this something >> that is just inherently going to be a bit messy? >> > > I can't see any way around topology hacking. If you need different > parameters, you need a different topology. It's going to be a bit messy, > and I would encourage you to give some serious thought to the potential > pitfalls I listed above. > > -Justin > >> Thanks very much for any insight or guidance you can offer! >> > > -- > > > 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 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Pressure Fluctuations
Dear users, Upon was trying to simulate an npt ensemble (protein in water), pressure was coupled using parinello rahman system with tau_p = 2, tau_t = 1; compressibility 4.5e-5, type = isotropic. (cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9; rcoulomb = 1.2; rlist = 1.2). No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3, 3.5), the pressure fluctuations are very drastic. I have gone through the mailing list regarding this issue but could not come to any conclusion. Any suggestions are helpfull. This is one of the statistics for pressure fluctuations. Statistics over 51 steps [ 0. through 1000. ps ], 1 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- Pressure5.77629 0.99398.013 -5.34218 (bar) Thanking you With Regards M. Kavyashree -- 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] g_membed tool
Dear all.. I am using g_membed tools to embed the protein into lipid membrane. I read that before doing g_membed we need to run a short run with some options in .mdp files. what are the steps do we need to do before g_membed. It is given that box size should be taken from the membrane strucuture file but i don t know how and where to mention the size? Whether any tutorial is available for transmembrane protein using g_membed tool? Thank you Mohanalakshmi N. -- 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] LINCS and number of nodes
On 16/03/11, Moeed wrote: > Dear experts, > > I am trying to build up a polymer in hexane system by increasing the density. > This seems to have been taking months. Why aren't you using genbox on your polymer starting configuration and an equilibrated box of hexane of the right density? Mark > After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS > and 1-4 warnings (even for NVT) which were not because of flawed topology > file. It turned out that simulations crashed just because of using -np > 4. > But still even with this -np, NPT did not work which made me to swtich to > berendsen from parrinelo rahman scheme. As I approched the desired density > again simulation crashed, so I used > > > trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300 > > to extract one of the frames before crash I did another NVT to equilibrate. > mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT3-frame2300_md -s -o -c -g -e > -x -v -pd > > > after around 1 ns I get the error below ( mdp file is also included). I > described above since I encountered the situation where root cause of problem > was not topology and just the computational issue ( I mean -np), I am just > curious if the same thing applies here. Please help me with this. Thank you > in advance. > > > more details: There is only one polyethylene chain ( 60 units) in 110 hexane. > The chain is not convoluted and has a little extended shape, which make it > not easy fit in the box. > > Moeed > === > > > step 449800, will finish Tue Mar 15 11:23:55 2011 > step 449900, will finish Tue Mar 15 11:23:55 2011 > [node5:09563] *** Process received signal *** > [node5:09563] Signal: Segmentation fault (11) > [node5:09563] Signal code: Address not mapped (1) > > [node5:09563] Failing at address: 0x80849dc0 > [node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10] > [node5:09563] [ 1] mdrun_mpi [0x4f0155] > [node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d) [0x4f9c1d] > > [node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8) [0x49c658] > [node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19] > [node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353] > [node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07] > > [node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319] > [node5:09563] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994] > [node5:09563] [ 9] mdrun_mpi [0x420449] > [node5:09563] *** End of error message *** > > -- > mpirun noticed that process rank 0 with PID 9563 on node node5.reyclus.loc > exited on signal 11 (Segmentation fault). > --- > > > > > pbc = xyz > ;energygrps = PE HEX > > ; Run control > integrator = md > dt = 0.002 > > nsteps = 100 ;5000 > nstcomm = 100 > > ; Output control > nstenergy = 100 > nstxout = 100 > nstvout = 0 > > nstfout = 0 > nstlog = 1000 > nstxtcout = 1000 > > ; Neighbor searching > nstlist = 10 > ns_type = grid > > > ; Electrostatics/VdW > coulombtype = PME > vdw-type = Shift > rcoulomb-switch = 0 > rvdw-switch = 0.9 ;0 > > > ; Cut-offs > rlist = 1.25 > rcoulomb = 1.25 ;1.1 > rvdw = 1.0 > > ; PME parameters > fourierspacing = 0.12 > > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > > ; Temperature coupling > > Tcoupl = v-rescale > tc-grps = System ;HEX > tau_t = 0.1 ;0.1 > ref_t = 300 ;300 > > ; Pressure coupling > > Pcoupl = no;berendsen > Pcoupltype = isotropic > tau_p = 0.5 ;0.5 > compressibility = 4.5e-5 4.5e-5 > ref_p = 30 30 > > > ; Velocity generation > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > ; Bonds > constraints = all-bonds > > constraint-algorithm = lincs > > > > -- gmx-
Re: [gmx-users] (no subject)
Алексей Раевский wrote: Hi, I have got a situation and I don't know how to cope with it. I carried out a simulation in gromacs 4.5.3 and the objects are protein, rna, water...The idea is that one atom part of rna has to create an h-bond with a water molecule, which at the same time makes h-bonds with aminoacids of the binding site. Something like a coordination molecule. So a command g_dist with index file and distance 0.35 showed me a number of water molecule I needed. But when I decided to visualize this process I saw that my protein with rna went out from the water box to another "cell" and the part of rna sppeared in the bottom of this box (( as I know this is not a bug or error of pbc. But i don't understand what is happening. Does my water forms bonds with this part and aminoacids (!!!) of binding site, because when I've converted trr to pdb with index file (atoms of binding site, part of rna, water molecules I've got with g_dist) I saw water molecules with part of rna in the bottom of display and binding site in the top...I tried to use -pbc nojump and center, -pbc mol...this flags united protein, rna and part of rna togetrher, but my water is not there Thank you For proper visualization, there is a workflow here: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions For complex systems, multiple iterations of trjconv are almost certainly required, some or all of which might need custom index groups. Bridging and simultaneous hydrogen bonds have been discussed frequently in the last few weeks. Have a look through the list archive. g_dist and g_hbond are the proper tools, but multiple operations and your own post-processing of such data will be required to extract the information you need. -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
[gmx-users] Pull Error message
Hi, I'm running MD on a 30x30x7,5nm system in which I pull two proteins away from each other. I have successfully pulled them apart to 9.4nm. But when I now use a pull_init1 = 9.59 pull_start = no pull_rate1 = 0 pull_dim = Y Y Y At one point, I get the following error message : Distance of pull group 1 (3.637819 nm) is larger than 0.49 times the box size (13.774273). The mdlib/pull.c code (l 329) shows that the 13.77423 value is ~ the squared value of half the smallest box vector ( wouldn't it be clearer to add a sqrt ?). So I don't understand why I get the error message, especially now. If maximum distance is the shortest box vector, I wouldn't have been able to pull it to 9.59nm. And if each dimensions are treated separately, I should not get this error as the Z component of the distance is less than 1nm. Any suggestions ? Thanks ! Jonathan. -- Message envoyé via le Webmail de l'IFR88 (http://www.ifr88.cnrs-mrs.fr). -- 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] (no subject)
Hi, I have got a situation and I don't know how to cope with it. I carried out a simulation in gromacs 4.5.3 and the objects are protein, rna, water...The idea is that one atom part of rna has to create an h-bond with a water molecule, which at the same time makes h-bonds with aminoacids of the binding site. Something like a coordination molecule. So a command g_dist with index file and distance 0.35 showed me a number of water molecule I needed. But when I decided to visualize this process I saw that my protein with rna went out from the water box to another "cell" and the part of rna sppeared in the bottom of this box (( as I know this is not a bug or error of pbc. But i don't understand what is happening. Does my water forms bonds with this part and aminoacids (!!!) of binding site, because when I've converted trr to pdb with index file (atoms of binding site, part of rna, water molecules I've got with g_dist) I saw water molecules with part of rna in the bottom of display and binding site in the top...I tried to use -pbc nojump and center, -pbc mol...this flags united protein, rna and part of rna togetrher, but my water is not there Thank you -- 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] Zero Potential of Mean Force with g_wham
Hi, please use g_wham 4.5.2 or later. We largely updated g_wham recently. If you get a flat PMF, check the warnings that g_wham gives you and --very important-- look at the histograms. That usually gives you a clue where the histograms to not overlap. In case you find a bug, please let me know. Otherwise, I have computed hundreds of PMFs with g_wham and it always worked fine. Cheers, Jochen On 3/9/11 Mar 9,11:08 PM, chris.ne...@utoronto.ca wrote: g_wham is not the only version of wham. Try using alan grossfield's version. Too often, I am afraid, gromacs accessory programs get broken in an update (not sure what the general solution is here beyond renewed calls for a proper test suite. Perhaps having 20+ programs is not ideal for a single software suite where the real focus is only on mdrun and grompp?) Chris. -- original message -- Hi, I ran g_wham 4.5.2 and did get a non-zero PMF curve. I assume that there is something going on with g_wham on version 4.5.1. Thank you for your help. Susana On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham anu.edu.au>wrote: -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell& Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] g_wham PMF profile
The reliability of the PMF curve depends on the reliability of sampling. If you're over-sampling in some regions along the reaction coordinate and under-sampling in others, then the weighting is probably wrong and the result inaccurate. I can't tell exactly from your description what's going on, but if you have largely overlapping histograms, then your window spacing and/or force constant settings are inappropriate. I don't really agree with the last point (with the first I fully agree). In my experience it helps a lot if you have multiple overlapping histograms. If each histograms overlaps only with the two neighbors, you typically get large uncertainties - even worse, since you usually don't know the autocorrelation time, you cannot even estimate your uncertainty. In addition, I don't see any reason why WHAM should have problems in case of largely overlapping histograms. My strong suggestion is to use as many histograms as possible, such that multiple histograms overlap. Make sure (if possible) that each histogram is independent by starting from independent initial frames (if these are available). Then you can use the boostrap of complete histograms (using the so-called Bayesian bootstrap) to compute the uncertainty: g_wham -nBootstrap 100 *-bs-method *b-hist ... As David just pointed out, please have a look into our recent paper: http://pubs.acs.org/doi/abs/10.1021/ct100494z Jochen S. Hub, Bert de Groot and David van der Spoel: g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates J. Chem. Theory Comput. 6 pp. 3713-3720 (2010) Cheers, Jochen -- --- Dr. Jochen Hub Computational and Systems Biology Dept. of Cell& Molecular Biology Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46-18-4715056 Fax: +46-18-511755 http://xray.bmc.uu.se/~jochen/index.html --- -- 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] Replacing a residue and continuing a simulation run
J. Nathan Scott wrote: Hello all, I was wondering, is it possible to replace a residue and then continue a simulation using the new parameters/geometry of the new residue? The reason I ask is that I am interested in performing simulations of proteins with tryptophan in its excited state following a lengthy equilibration with TRP in its ground state. I already have reliable excited state atomic charges for the TRP atoms, and I suppose that I will need to change at least some bonded terms to account for the altered geometry of the excited state. I am still in the middle of reading the information that is out there regarding parameterizing new molecules (since I'm using the CHARMM FF, I've been starting to follow Alexander MacKerell's protocols), but I'm still not quite sure as to how one would practically do this residue replacement in the context of a Gromacs run. Will I need to manually edit my .top file, or is there perhaps another way to update the topology file with the new residue following the ground state equilibration? How about coordinates, will I need to transform the TRP coordinates to the excited state geometry by hand? You would have to hack the topology. Coordinates are another matter. If you start making ad hoc changes, then what's the point of a continuation? Presumably, if you've designed the residue's topology correctly (including both bonded and nonbonded parameters), then the residue will adopt the correct geometry on its own. The complication comes with bonded interactions. Are you using constraints? If so, then changing bond lengths will cause the constraints to fail at step 0 (or very soon thereafter) and the simulation will crash. You can get around this by setting "continuation = no" in the .mdp file, but again I wonder what the value of the continuation is. You'd almost certainly have to forgo the use of .cpt files, supplying instead your .trr and .edr files to preserve as much of the previous ensemble as possible. Even if you're not using constraints, the simulation may still fail if you're suddenly changing bond lengths, angles, etc by anything more than a very small amount. Perhaps the most important question: is there a better way to do the sort of residue replacement I'm contemplating, or is this something that is just inherently going to be a bit messy? I can't see any way around topology hacking. If you need different parameters, you need a different topology. It's going to be a bit messy, and I would encourage you to give some serious thought to the potential pitfalls I listed above. -Justin Thanks very much for any insight or guidance you can offer! -- 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] Replacing a residue and continuing a simulation run
Hello all, I was wondering, is it possible to replace a residue and then continue a simulation using the new parameters/geometry of the new residue? The reason I ask is that I am interested in performing simulations of proteins with tryptophan in its excited state following a lengthy equilibration with TRP in its ground state. I already have reliable excited state atomic charges for the TRP atoms, and I suppose that I will need to change at least some bonded terms to account for the altered geometry of the excited state. I am still in the middle of reading the information that is out there regarding parameterizing new molecules (since I'm using the CHARMM FF, I've been starting to follow Alexander MacKerell's protocols), but I'm still not quite sure as to how one would practically do this residue replacement in the context of a Gromacs run. Will I need to manually edit my .top file, or is there perhaps another way to update the topology file with the new residue following the ground state equilibration? How about coordinates, will I need to transform the TRP coordinates to the excited state geometry by hand? Perhaps the most important question: is there a better way to do the sort of residue replacement I'm contemplating, or is this something that is just inherently going to be a bit messy? Thanks very much for any insight or guidance you can offer! -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- 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] OPLS forcefield for Alkane and ethers?
Sanku M wrote: Hi, I was wondering whether OPLS supports force-field for alkane chain or ethers . One of the molecule I am looking forward to using is ethylene glycol ( CH2-O-CH2-O-CH2 ). But, I was wondering whether it is available in OPLS forcefield . Practically speaking, if you can develop reliable parameters, you can use any force field you like. Whether or not parameters already exist for this particular purpose (or a suitably similar one) should be documented in the literature. As for whether or not these kinds of polymers are already implemented in Gromacs, the answer is almost certainly no, but the framework is there so that you can introduce whatever new species you want. http://www.gromacs.org/Documentation/How-tos/Polymers -Justin Any help will be appreciated . Sanku -- 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] OPLS forcefield for Alkane and ethers?
On 2011-03-15 21.30, Sanku M wrote: Hi, I was wondering whether OPLS supports force-field for alkane chain or ethers . One of the molecule I am looking forward to using is ethylene glycol ( CH2-O-CH2-O-CH2 ). But, I was wondering whether it is available in OPLS forcefield . Any help will be appreciated . Sanku Yes. Check oplsaa.ff/atomtypes.atp and oplsaa.ff/ffnonbonded.itp -- 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
[gmx-users] OPLS forcefield for Alkane and ethers?
Hi, I was wondering whether OPLS supports force-field for alkane chain or ethers . One of the molecule I am looking forward to using is ethylene glycol ( CH2-O-CH2-O-CH2 ). But, I was wondering whether it is available in OPLS forcefield . Any help will be appreciated . Sanku -- 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] Forces with Constraints
Hello GROMACS users, I am trying to compute PMF profile for water by integrating the force profile along a given direction. I take the forces directly from MD. I am using SETTLE for constraining the geometry of water molecules (SPC/E model). My question is that do these forces include the constraint forces or are these simply the forces on individual atoms at a given snapshot. If they do not include the constraint forces, then is there a way to include it because it might affect the dynamics. Thanks. Apoorv -- 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] g_order for DPC alkyl chain in the micelle
Hi very recently I faced the same problem with a system that gives micelles of different geometries and, as far as I saw, g_order don't do that. Then I decided to compute a kind of local order parameters defined as: S_i=(3 cos(\theta)-1)/2 where theta is the angle between the segments joining the carbon atoms (i-1,i+1) and (i, i+2) in a linear C-chain. Perhaps you find this reasonable for your analysis... Cheers, Ángel. On Mon, 2011-03-14 at 18:25 +0100, sa wrote: > Dear all, > > I would like to compute the order parameter tensor elements of a DPC > micelle with respect to a vector direction (for example the vector > from the > center of mass of the micelle to the phosphorus atom). It is possible > with g_order (4.5.3). if yes how ? > > Thank you in advance. > > > > -- > 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
[gmx-users] Re: pull forces
Message: 5 Date: Tue, 15 Mar 2011 07:17:28 -0700 (PDT) From: Michael Brunsteiner Subject: [gmx-users] pull forces To: gmx users Message-ID:<613152.30411...@web120517.mail.ne1.yahoo.com> Content-Type: text/plain; charset=us-ascii Dear all, does anybody know what the forces that are saved in the f*xvg files from the pull-code actually are? are these: 1) the (sum of the) forces due to the normal non-bonded interactions in the system acting on the ref and the the full groups. 2) only the forces from the harmonic restraint. 3) the sum of both? if you mean the pullf.xvg it's 2. only the force from the harmonic restraint (if you're using 'pull=umbrella') i just did a test writing out the forces from the trajectory file, and looking at the relevant forces (the ones in the z-dimension in my case, as i use pulldim N N Y and constrain the groups to stay put in the x and y dimensions) it seems as if the forces on the pull group are oscillating as expected, but the forces on the reference group are close to, but not exactly(!) zero. i am not sure how to interpret this ... cheers Michael -- 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] LINCS and number of nodes
Moeed wrote: Dear experts, I am trying to build up a polymer in hexane system by increasing the density. After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS and 1-4 warnings (even for NVT) which were not because of flawed topology file. It turned out that simulations crashed just because of using -np > 4. But still even with this -np, NPT did not work which made me to swtich to berendsen from parrinelo rahman scheme. As I approched the desired density again simulation crashed, so I used trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300 to extract one of the frames before crash I did another NVT to equilibrate. mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT3-frame2300_md -s -o -c -g -e -x -v -pd after around 1 ns I get the error below ( mdp file is also included). I described above since I encountered the situation where root cause of problem was not topology and just the computational issue ( I mean -np), I am just curious if the same thing applies here. Please help me with this. Thank you in advance. What MPI library (and version) are you using? Do your runs work in serial? more details: There is only one polyethylene chain ( 60 units) in 110 hexane. The chain is not convoluted and has a little extended shape, which make it not easy fit in the box. What do you mean it doesn't fit in the box? If you've got a system that you're trying to force into some shape or size, your PE chain is probably just crashing into itself across periodic boundaries. Watch the trajectory to see what's going on prior to the crash. -Justin Moeed === step 449800, will finish Tue Mar 15 11:23:55 2011 step 449900, will finish Tue Mar 15 11:23:55 2011 [node5:09563] *** Process received signal *** [node5:09563] Signal: Segmentation fault (11) [node5:09563] Signal code: Address not mapped (1) [node5:09563] Failing at address: 0x80849dc0 [node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10] [node5:09563] [ 1] mdrun_mpi [0x4f0155] [node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d) [0x4f9c1d] [node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8) [0x49c658] [node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19] [node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353] [node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07] [node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319] [node5:09563] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994] [node5:09563] [ 9] mdrun_mpi [0x420449] [node5:09563] *** End of error message *** -- mpirun noticed that process rank 0 with PID 9563 on node node5.reyclus.loc exited on signal 11 (Segmentation fault). --- pbc = xyz ;energygrps = PE HEX ;Run control integrator = md dt = 0.002 nsteps = 100 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.25 rcoulomb= 1.25 ;1.1 rvdw= 1.0 ;PME parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;Temperature coupling Tcoupl = v-rescale tc-grps = System ;HEX tau_t = 0.1 ;0.1 ref_t = 300 ;300 ;Pressure coupling Pcoupl = no;berendsen Pcoupltype = isotropic tau_p = 0.5;0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 3030 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry
[gmx-users] LINCS and number of nodes
Dear experts, I am trying to build up a polymer in hexane system by increasing the density. After PR step, my NVT and NPT trailes failed. Initially I used to get LINCS and 1-4 warnings (even for NVT) which were not because of flawed topology file. It turned out that simulations crashed just because of using -np > 4. But still even with this -np, NPT did not work which made me to swtich to berendsen from parrinelo rahman scheme. As I approched the desired density again simulation crashed, so I used trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300 to extract one of the frames before crash I did another NVT to equilibrate. mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT3-frame2300_md -s -o -c -g -e -x -v -pd after around 1 ns I get the error below ( mdp file is also included). I described above since I encountered the situation where root cause of problem was not topology and just the computational issue ( I mean -np), I am just curious if the same thing applies here. Please help me with this. Thank you in advance. more details: There is only one polyethylene chain ( 60 units) in 110 hexane. The chain is not convoluted and has a little extended shape, which make it not easy fit in the box. Moeed === step 449800, will finish Tue Mar 15 11:23:55 2011 step 449900, will finish Tue Mar 15 11:23:55 2011 [node5:09563] *** Process received signal *** [node5:09563] Signal: Segmentation fault (11) [node5:09563] Signal code: Address not mapped (1) [node5:09563] Failing at address: 0x80849dc0 [node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10] [node5:09563] [ 1] mdrun_mpi [0x4f0155] [node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d) [0x4f9c1d] [node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8) [0x49c658] [node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19] [node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353] [node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07] [node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319] [node5:09563] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994] [node5:09563] [ 9] mdrun_mpi [0x420449] [node5:09563] *** End of error message *** -- mpirun noticed that process rank 0 with PID 9563 on node node5.reyclus.loc exited on signal 11 (Segmentation fault). --- pbc = xyz ;energygrps = PE HEX ;Run control integrator = md dt = 0.002 nsteps = 100 ;5000 nstcomm = 100 ;Output control nstenergy = 100 nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 1000 nstxtcout = 1000 ;Neighbor searching nstlist = 10 ns_type = grid ;Electrostatics/VdW coulombtype = PME vdw-type= Shift rcoulomb-switch = 0 rvdw-switch = 0.9 ;0 ;Cut-offs rlist = 1.25 rcoulomb= 1.25 ;1.1 rvdw= 1.0 ;PME parameters fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ;Temperature coupling Tcoupl = v-rescale tc-grps = System ;HEX tau_t = 0.1 ;0.1 ref_t = 300 ;300 ;Pressure coupling Pcoupl = no;berendsen Pcoupltype = isotropic tau_p = 0.5;0.5 compressibility = 4.5e-5 4.5e-5 ref_p = 3030 ;Velocity generation gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ;Bonds constraints = all-bonds constraint-algorithm = lincs -- 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] Umberella sampling
1. Depends on how you set them in your .mdp file. It could be either. 2. There is no general method. Use trial and error. Also, your question is flawed, K defines X. Unless by "length of one windows" you meant the distance between neighbouring centers of restraint (umbrellas). 3. you need overlapping distributions. Let's leave it at that. I have not seen any general treatment of what K is required and I am rather sure that it is impossible to predetermine the necessary force constants (K) unless you know the PMF. If you need to know the PMF beforehand then this is not a general solution and also probably useless since the whole purpose is to get the PMF. Chris. -- original message -- Dear All afew question in umberella sampling tutorial: 1-We do umberella sampling for each of 25 simulation windows,while using a spring(harmonic potential),Are these springs 1 or 3 dimensional? 2-Suppose the length of one windows is X nm,what is the approperiate K (spring constant) for this window?Is there a general way to determine this value? 3-I think the K must be such that the oscilation amplitude be a few larger than X/2, because we need overlapping of density distribution for analysing with wham method, am I right? Thanks in advance -- 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] Pulling
1. yes. it is acceptable. It is different, but neither method is de facto better. 2. to enhance convergence by limiting the amount of phase space that must be sampled. Changing the restraints can change the profile, but if you care only about the integrated standard binding free energy then it does not change the converged result. See, for example, D. L. Mobley, J. D. Chodera, K. A. Dill. "On the use of orientational restraints and symmetry number corrections in alchemical free energy calculations", ... Chris. -- original message -- Dear All Afew question about Pulling in Umberella Sampling 1-the goal of pulling is making some primary structures (in different distances) to do umberella sampling for each one of them. I can make these states by transporting my ligands along a vector to prepare these primary structures.Is this correct?Now I can do US for each one!without any need to doing pulling. 2-Why do we keep fix the relative orientation of Protein-ligand during the pulling ? I think changing the orientation of ligand during the pulling(suppose the protein is restrain) can chang our result? Because our umbrella sampling maintain this orientation too.am I right? Thanks in advance -- next part -- -- 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] Re: surface tension
Dear Elisabeth, PBC are still there when you increase the box length in one direction, but that increase creates an empty region between the periodic images. provided the empty region is large enough (larger than cutoff values, for instance), periodicity no longer affects the system during a typical MD simulation, except for the other two directions. as regards long range corrections, either do not use them at all or choose a two dimensional correction (see the manual). and try some google search on the simulation of Langmuir films. for instance, I wrote this paper a while ago: Molecular Dynamics Simulation of a Perylene-Derivative Langmuir Film André F. de Moura and Milan Trsic J. Phys. Chem. B, 2005, 109 (9), pp 4032–4041 DOI: 10.1021/jp0452711 best Andre On Tue, Mar 15, 2011 at 1:52 AM, Elisabeth wrote: > Dear Andre, > > Thanks for the helpful information. > > I need to do some text reading to understand the periodic BC effect you are > talking about. I dont see why increasing length in z direction does not lead > to periodic BC in z and only for x, y ? does that mean the thickness of > layer would be the Z dimension? then how much increase in one direction is > reasonable? (If I have a 2 nm box). > > Also Can you please introduce some text book? > > Thank you, > Best regards, > > 2011/3/15 André Farias de Moura >> >> Dear Elisabeth, >> >> actually, it is the other way around, you need increase the box length in >> one direction, thus keeping periodic boundary conditions in the other two >> directions while a (infinitely periodic) surface is created. and notice >> that >> using genconf with -nbox 3 3 1 will increase your system but will not make >> it a surface system, unless you increase the box length in one direction. >> >> as regards the size, the larger the model system, the smaller should be >> the fluctuations. but mind that you should increase the size by a few >> order of magnitude for any noticeable decrease on the (huge) RMSD >> values you are getting. if you want to check the results for convergence >> maybe you could try either a block averaging or a running average (grace >> can do that for you). >> >> best regards >> >> Andre >> >> On Mon, Mar 14, 2011 at 7:57 PM, Elisabeth wrote: >> > Hello, >> > >> > Thank you for your answer. >> > >> > 1- If I am right I have to increase the length in two directions rather >> > than >> > one, to create a plane parallel to XY for example? >> > >> > 2- Can you please give me an idea on how many molecules I need to have >> > in >> > the box and also what should be the thickness of layer? I have now 3nm X >> > 9 X >> > 9 dimensions. That is thickness of 3nm. What I did was replicating a 3nm >> > box >> > using genconf -nbox 3 3 1. I dont know what is the correct way of >> > creating a >> > layer for surface tension calculation. >> > >> > I appreciate any comments about number of molecules, box dimensions for >> > such >> > a study. >> > >> > 3- my last question is how can I make sure surface tension reported by >> > g_energy is the equilibrated one. RMSD is very big compared to surf. >> > ten. ! >> > >> > Thanks for your time. >> > Elisabeth >> > >> > ** >> > >> > if you are interested in the surface tension of a pure liquid, which I >> > assume is >> > true from your message, then you need to create at least one surface, >> > since >> > periodic boundary conditions make the model system infinite, i.e., >> > without a >> > surface whatsoever. >> > >> > the easiest way to make that happen is to increase the length of the box >> > in >> > one direction, say the z direction. that way you will end up with a >> > system >> > that >> > resemble a (thin) liquid film with vacuum below and above, meaning that >> > you >> > now have two surfaces. run a regular simulation (NVT) e use g_energy to >> > get >> > the surface tension. >> > >> > btw: as any other pressure related property, fluctuations are huge. >> > >> > best >> > >> > Andre >> > >> > On Wed, Mar 9, 2011 at 12:25 PM, Elisabeth wrote: >> >> Dear gmx users, >> >> >> >> Since I am new to surface tension topic I need to ask very trivial >> >> questions. Please help me out with these simple questions. >> >> >> >> As a starting point I am going to calculate surface tension of a pure >> >> alkane >> >> in a cubic box and compare with experimental values. >> >> >> >> 1- g_energy is giving #Surf*SurfTen by default. On the other hand >> >> surface >> >> tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e >> >> Pres-XX-(bar), Pres-YY(bar), Pres--(bar) >> >> >> >> Can anyone tell me what the difference between these two is? >> >> >> >> 2- In pressure coupling settings there is surface_tension option which >> >> I >> >> guess is applicable where surface tension needs to be kept fixed. If >> >> one >> >> want to calculate surface tension I dont think this option make sense. >> >> Am >> >> I >> >> right? >> >> >> >> 3- I am using the following setting: I
[gmx-users] pull forces
Dear all, does anybody know what the forces that are saved in the f*xvg files from the pull-code actually are? are these: 1) the (sum of the) forces due to the normal non-bonded interactions in the system acting on the ref and the the full groups. 2) only the forces from the harmonic restraint. 3) the sum of both? i just did a test writing out the forces from the trajectory file, and looking at the relevant forces (the ones in the z-dimension in my case, as i use pulldim N N Y and constrain the groups to stay put in the x and y dimensions) it seems as if the forces on the pull group are oscillating as expected, but the forces on the reference group are close to, but not exactly(!) zero. i am not sure how to interpret this ... cheers Michael -- 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] Pulling
Dear All Afew question about Pulling in Umberella Sampling 1-the goal of pulling is making some primary structures (in different distances) to do umberella sampling for each one of them. I can make these states by transporting my ligands along a vector to prepare these primary structures.Is this correct?Now I can do US for each one!without any need to doing pulling. 2-Why do we keep fix the relative orientation of Protein-ligand during the pulling ? I think changing the orientation of ligand during the pulling(suppose the protein is restrain) can chang our result? Because our umbrella sampling maintain this orientation too.am I right? Thanks in advance -- 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] Grandcanonical Ensemble
On 16/03/11, mohsen ramezanpour wrote: > Dear All > > 1-Does Gromacs support Grandcanonical ensemble too? > No. The number of particles is fixed at grompp time. > 2-I want to increase the length of my simulation box during simulation,Is it > possible? > Only via pressure-coupling. > 3-As a result.I want to do my simulation in grandcanonical in the following > way: > > As the length of my simulation box is increasing,I want to full the new > volume with water molecules.Is this possible with Gromacs? > No. Mark -- 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] Umberella sampling
Dear All afew question in umberella sampling tutorial: 1-We do umberella sampling for each of 25 simulation windows,while using a spring(harmonic potential),Are these springs 1 or 3 dimensional? 2-Suppose the length of one windows is X nm,what is the approperiate K (spring constant) for this window?Is there a general way to determine this value? 3-I think the K must be such that the oscilation amplitude be a few larger than X/2, because we need overlapping of density distribution for analysing with wham method, am I right? Thanks in advance -- 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] Grandcanonical Ensemble
Dear All 1-Does Gromacs support Grandcanonical ensemble too? 2-I want to increase the length of my simulation box during simulation,Is it possible? 3-As a result.I want to do my simulation in grandcanonical in the following way: As the length of my simulation box is increasing,I want to full the new volume with water molecules.Is this possible with Gromacs? Thanks in advance Mohsen -- 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] Failure to preserve simulation temperature
NG HUI WEN wrote: Hi all, I have something here which I am would like to pick your brains. Thank you in advance. In my trial-and-error attempt to equilibrate my membrane protein system, I encountered this problem. I was playing with 2 different mdp files (in succession), first by using the Nose Hoover then v-rescale. I realised upon changing from the former to the latter there was a drop in simulation temperature from 310K to about 263K. Not sure if this have anything to do with the switch of thermostat or due to some other parameter change? The mdp file below which contain the Nose Hoover thermostat was used to generate A3_1posre (see below grompp command) title = NPT define = -DPOSRES ; Run parameters integrator = md nsteps = 50; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; Output control nstxout = 5 nstvout = 5 nstenergy = 500 nstlog = 500 ; Bond parameters continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = Nose-Hoover tc-grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel = no ; COM motion removal nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPC SOL_CL- ; Energy groups energygrps = Protein POPC SOL_CL- I then use another mdp file containing v-rescale thermostat to extend the simulation grompp –f v-rescale.mdp–c A3_1posre.gro –o A3_noposre.tpr -n index.ndx -p topol_3.top mdrun_mpi -s A3_noposre.tpr-v -cpi A3_1posre.cpt The problem is likely here. You're switching the conditions of the ensemble during mdrun. Normally, you would supply the .cpt file to grompp -t to preserve all the state variables. In conjunction with "gen_vel = no" in the .mdp file, the continuation is exact. Since you're not generating velocities with grompp AND not supplying a .cpt file, the initial state will be hard to predict, but likely will not correspond to the proper ensemble. -Justin title = NPT define = ; Run parameters integrator = md nsteps = 100 ; 2 * 100 = 2000 ps (2 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 25 nstvout = 25 nstenergy = 1000 nstlog = 500 nstxtcout = 25 ; Bond parameters continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 10 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.12 ; Temperature coupling is on tcoupl = v-rescale fluctuation tc-grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel = no ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPC SOL_CL- ; Energy groups energygrps = Protein POPC SOL_CL- << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this
[gmx-users] Failure to preserve simulation temperature
Hi all, I have something here which I am would like to pick your brains. Thank you in advance. In my trial-and-error attempt to equilibrate my membrane protein system, I encountered this problem. I was playing with 2 different mdp files (in succession), first by using the Nose Hoover then v-rescale. I realised upon changing from the former to the latter there was a drop in simulation temperature from 310K to about 263K. Not sure if this have anything to do with the switch of thermostat or due to some other parameter change? The mdp file below which contain the Nose Hoover thermostat was used to generate A3_1posre (see below grompp command) title = NPT define = -DPOSRES ; Run parameters integrator = md nsteps = 50; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; Output control nstxout = 5 nstvout = 5 nstenergy = 500 nstlog = 500 ; Bond parameters continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 5 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = Nose-Hoover tc-grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel = no ; COM motion removal nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPC SOL_CL- ; Energy groups energygrps = Protein POPC SOL_CL- I then use another mdp file containing v-rescale thermostat to extend the simulation grompp -f v-rescale.mdp-c A3_1posre.gro -o A3_noposre.tpr -n index.ndx -p topol_3.top mdrun_mpi -s A3_noposre.tpr-v -cpi A3_1posre.cpt title = NPT define = ; Run parameters integrator = md nsteps = 100 ; 2 * 100 = 2000 ps (2 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 25 nstvout = 25 nstenergy = 1000 nstlog = 500 nstxtcout = 25 ; Bond parameters continuation= yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 10 rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.12 ; Temperature coupling is on tcoupl = v-rescale fluctuation tc-grps = Protein POPC SOL_CL- tau_t = 0.1 0.1 0.1 ref_t = 310 310 310 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-54.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; Velocity generation gen_vel = no ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_POPC SOL_CL- ; Energy groups energygrps = Protein POPC SOL_CL- << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you a
Re: [gmx-users] Re: installation of gromacs (Dommert Florian)
On Tue, 2011-03-15 at 05:53 +0100, Thomas Koller wrote: > > I have installed Gromacs but if I want to open another terminal and > run another simulation it does not work. You have to make sure, that the binaries and libraries installed in $GROMACS/bin and $GROMACS/lib are found by the terminal, which can be achieved by sourcing the corresponding GMXRC file. Actually it should work like source $GROMACS/bin/GMXRC However I experienced a hanging terminal for this procedure, but if you choose the script corresponding to your type of console (on Ubuntu you will usually use bash), it should work. So just put the line . $GROMACS/bin/GMXRC.bash or source $GROMACS/bin/GMXRC.bash in your .bashrc (do not forget the "." at the beginning of the line), open a new terminal and type: which mdrun This should give you: $GROMACS/bin/mdrun If it does, everything is fine and you can have fun with Gromacs, otherwise post your output, that you can get help. /Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] isopeptide bond
On 15/03/11, Yulian Gavrilov wrote: > Thanks! I understand it, but I had several errors about it. Without adding of > (HP CT N) [angletype] it does not work. How to force it to take its type > from its current environment, not its historical one? > > Your .rtp and .hdp specify the atom types. Mark > > > > 2011/3/15 Mark Abraham > > > > > > > > > On 15/03/11, Yulian Gavrilov wrote: > > > > > > Dear Mark, > > > Thank you for your help! Now it works! I made MD without errors. > > > I changed N3 to N, add one additional [angletype] to .itp (HP CT N) > > > and removed one of HZ1 from Lys that participate in isopeptide bond; made > > > appropriate changes in .atp, .hdp, .rtp and specbond.dat. > > > > > > > > > > > > > > > Good. Like I've said a few times, you have a normal peptide bond and those > > interaction types all exist already; you do not need to add more > > interaction types. Look up in the .rtp what the HP atom type is used for. > > The H atom on the N should take its type from its current environment, not > > its historical one. Until your peptide bond resembles a backbone peptide in > > *all* particulars, it is not a well-modeled peptide bond. > > > > > > Mark > > > > > > > > > > > > 2011/3/14 Mark Abraham > > > > > > > > > > > > > > > > > > > > > > > On 14/03/11, Yulian Gavrilov wrote: > > > > > > > > > > > > > > > Dear, Mark > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > You asking about this (?): > > > > > > > > > > > > > > > > > > > > According to ffamber99.atp: > > > > > > > > > > > > > > > amber99_3414.01000; N sp2 > > > > > nitrogen in amide groups > > > > > > > > > > > > > > > amber99_3914.01000; N3 sp3 N > > > > > for charged amino groups (Lys, etc) > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > If I don't mix, “N” is used in > > > > > peptide bond in amber99 and “N3” is used in Lys side chain. That > > > > > is why I didn't use backbone peptide. > > > > > > > > > > > > > > > > > > > > > > > > > > > N3 is used in a quaternary amine. N is used in an amide. Atom types are > > > > related to the chemical functional group they are *now* in, not what > > > > they were before a notional peptide condensation. You have an amide, > > > > and the nitrogen in it cannot be protonated. I said that in an email a > > > > fortnight ago. Use normal peptide parameters. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > [atoms] and [bonds] section for LYQ > > > > > and GLQ in topol.top > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > [ atoms ] > > > > > > > > > > > > > > > ; nr type resnr residue atom > > > > > cgnr charge mass typeBchargeB massB > > > > > > > > > > > > > > >750 amber99_34 48LYQ N > > > > > 748-0.4157 14.01 ; qtot -5.416 > > > > > > > > > > > > > > >751 amber99_17 48LYQ H > > > > > 749 0.2719 1.008 ; qtot -5.144 > > > > > > > > > > > > > > >752 amber99_11 48LYQ CA > > > > > 750 -0.07206 12.01 ; qtot -5.216 > > > > > > > > > > > > > > >753 amber99_19 48LYQ HA > > > > > 751 0.0994 1.008 ; qtot -5.116 > > > > > > > > > > > > > > >754 amber99_11 48LYQ CB > > > > > 752 -0.04845 12.01 ; qtot -5.165 > > > > > > > > > > > > > > >755 amber99_18 48LYQHB1 > > > > > 753 0.034 1.008 ; qtot -5.131 > > > > > > > > > > > > > > >756 amber99_18 48LYQHB2 > > > > > 754 0.034 1.008 ; qtot -5.097 > > > > > > > > > > > > > > >757 amber99_11 48LYQ CG > > > > > 7550.06612 12.01 ; qtot -5.031 > > > > > > > > > > > > > > >758 amber99_18 48LYQHG1 > > > > > 7560.01041 1.008 ; qtot -5.02 > > > > > > > > > > > > > > >759 amber99_18 48LYQHG2 > > > > > 7570.01041 1.008 ; qtot -5.01 > > > > > > > > > > > > > > >760 amber99_11 48LYQ CD > > > > > 758 -0.03768 12.01 ; qtot -5.048 > > > > > > > > > > > > > > >761 amber99_18 48LYQHD1 > > > > > 7590.01155 1.008 ; qtot -5.036 > > > > > > > > > > > > > > >762 amber99_18 48LYQHD2 > > > > > 7600.01155 1.008 ; qtot -5.025 > > > > > > > > > > > > > > >763 amber99_11 48LYQ CE > > > > > 7610.32604 12.01 ; qtot -4.699 > > > > > > > > > > > > > > >764 amber99_28 48LYQHE1 > > > > > 762 -0.03358 1.008 ; qtot -4.732 > > > > > > > > > > > > > > >765 amber99_28 48LYQHE2 > > > > > 763 -0.03358 1.008 ; qtot -4.766 > > > > > > > > > > > > > > >766 amber99_39 48LYQ
Re: [gmx-users] isopeptide bond
Thanks! I understand it, but I had several errors about it. Without adding of (HP CT N) [angletype] it does not work. How to force it to take its type from its current environment, not its historical one? 2011/3/15 Mark Abraham > > > On 15/03/11, *Yulian Gavrilov * wrote: > > Dear Mark, > Thank you for your help! Now it works! I made MD without errors. > I changed N3 to N, add one additional [angletype] to .itp (HP CT N) and > removed one of HZ1 from Lys that participate in isopeptide bond; made > appropriate changes in .atp, .hdp, .rtp and specbond.dat. > > > Good. Like I've said a few times, you have a normal peptide bond and those > interaction types all exist already; you do not need to add more interaction > types. Look up in the .rtp what the HP atom type is used for. The H atom on > the N should take its type from its current environment, not its historical > one. Until your peptide bond resembles a backbone peptide in *all* > particulars, it is not a well-modeled peptide bond. > > Mark > > > 2011/3/14 Mark Abraham > >> >> >> On 14/03/11, *Yulian Gavrilov * wrote: >> >> Dear, Mark >> >> You asking about this (?): >> >> According to ffamber99.atp: >> >> amber99_34 14.01000 ; N sp2 nitrogen in amide groups >> >> amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) >> >> If I don't mix, “N” is used in peptide bond in amber99 and “N3” is used >> in Lys side chain. That is why I didn't use backbone peptide. >> >> >> N3 is used in a quaternary amine. N is used in an amide. Atom types are >> related to the chemical functional group they are *now* in, not what they >> were before a notional peptide condensation. You have an amide, and the >> nitrogen in it cannot be protonated. I said that in an email a fortnight >> ago. Use normal peptide parameters. >> >> >> *[atoms] and [bonds] section for LYQ and GLQ in topol.top * >> >> [ atoms ] >> >> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB >> >> 750 amber99_34 48 LYQ N 748 -0.4157 14.01 ; qtot -5.416 >> >> 751 amber99_17 48 LYQ H 749 0.2719 1.008 ; qtot -5.144 >> >> 752 amber99_11 48 LYQ CA 750 -0.07206 12.01 ; qtot -5.216 >> >> 753 amber99_19 48 LYQ HA 751 0.0994 1.008 ; qtot -5.116 >> >> 754 amber99_11 48 LYQ CB 752 -0.04845 12.01 ; qtot -5.165 >> >> 755 amber99_18 48 LYQ HB1 753 0.034 1.008 ; qtot -5.131 >> >> 756 amber99_18 48 LYQ HB2 754 0.034 1.008 ; qtot -5.097 >> >> 757 amber99_11 48 LYQ CG 755 0.06612 12.01 ; qtot -5.031 >> >> 758 amber99_18 48 LYQ HG1 756 0.01041 1.008 ; qtot -5.02 >> >> 759 amber99_18 48 LYQ HG2 757 0.01041 1.008 ; qtot -5.01 >> >> 760 amber99_11 48 LYQ CD 758 -0.03768 12.01 ; qtot -5.048 >> >> 761 amber99_18 48 LYQ HD1 759 0.01155 1.008 ; qtot -5.036 >> >> 762 amber99_18 48 LYQ HD2 760 0.01155 1.008 ; qtot -5.025 >> >> 763 amber99_11 48 LYQ CE 761 0.32604 12.01 ; qtot -4.699 >> >> 764 amber99_28 48 LYQ HE1 762 -0.03358 1.008 ; qtot -4.732 >> >> 765 amber99_28 48 LYQ HE2 763 -0.03358 1.008 ; qtot -4.766 >> >> 766 amber99_39 48 LYQ NZ 764 -1.03581 14.01 ; qtot -5.801 >> >> 767 amber99_17 48 LYQ HZ1 765 0.38604 1.008 ; qtot -5.415 >> >> 768 amber99_17 48 LYQ HZ2 766 0.38604 1.008 ; qtot -5.029 >> >> >> Atom 766 is bound to two carbon atoms and two hydrogen atoms. There is no >> such thing as a quaternary amide nitrogen, and certainly AMBER does not have >> parameters for it. >> >> >> >> 769 amber99_2 48 LYQ C 767 0.5973 12.01 ; qtot -4.432 >> >> 770 amber99_41 48 LYQ O 768 -0.5679 16 ; qtot -5 >> >> >> >> 2440 amber99_34 152 GLQ N 2438 -0.4157 14.01 ; qtot -12.42 >> >> 2441 amber99_17 152 GLQ H 2439 0.2719 1.008 ; qtot -12.14 >> >> 2442 amber99_11 152 GLQ CA 2440 -0.0252 12.01 ; qtot -12.17 >> >> 2443 amber99_19 152 GLQ HA1 2441 0.0698 1.008 ; qtot -12.1 >> >> 2444 amber99_19 152 GLQ HA2 2442 0.0698 1.008 ; qtot -12.03 >> >> 2445 amber99_2 152 GLQ C 2443 0.5973 12.01 ; qtot -11.43 >> >> 2446 amber99_41 152 GLQ O 2444 -0.5679 16 ; qtot -12 >> >> >> >> [ bonds ] >> >> ; ai aj funct c0 c1 c2 c3 >> >> 750 751 1 >> >> 750 752 1 >> >> 752 753 1 >> >> 752 754 1 >> >> 752 769 1 >> >> 754 755 1 >> >> 754 756 1 >> >> 754 757 1 >> >> 757 758 1 >> >> 757 759 1 >> >> 757 760 1 >> >> 760 761 1 >> >> 760 762 1 >> >> 760 763 1 >> >> 763 764 1 >> >> 763 765 1 >> >> 763 766 1 >> >> 766 767 1 >> >> 766 768 1 >> >> 766 2445 1 >> >> >> OK, you have the N-C bond for the peptide link. >> >> >> 769 770 1 >> >> 769 771 1 >> >> >> >> 2440 2441 1 >> >> 2440 2442 1 >> >> 2442 2443 1 >> >> 2442 2444 1 >> >> 2442 2445 1 >> >> 2445 2446 1 >> >> >> Does 2445 make any other bonds? If not, how did you handle the chain >> termination? >> >> Mark >> -- >> 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
Re: [gmx-users] isopeptide bond
On 15/03/11, Yulian Gavrilov wrote: > Dear Mark, > Thank you for your help! Now it works! I made MD without errors. > I changed N3 to N, add one additional [angletype] to .itp (HP CT N) and > removed one of HZ1 from Lys that participate in isopeptide bond; made > appropriate changes in .atp, .hdp, .rtp and specbond.dat. > > Good. Like I've said a few times, you have a normal peptide bond and those interaction types all exist already; you do not need to add more interaction types. Look up in the .rtp what the HP atom type is used for. The H atom on the N should take its type from its current environment, not its historical one. Until your peptide bond resembles a backbone peptide in *all* particulars, it is not a well-modeled peptide bond. Mark > 2011/3/14 Mark Abraham > > > > > > > > > On 14/03/11, Yulian Gavrilov wrote: > > > > > > Dear, Mark > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > You asking about this (?): > > > > > > > > > > > > According to ffamber99.atp: > > > > > > > > > amber99_3414.01000; N sp2 > > > nitrogen in amide groups > > > > > > > > > amber99_3914.01000; N3 sp3 N > > > for charged amino groups (Lys, etc) > > > > > > > > > > > > > > > > > > > > > If I don't mix, “N” is used in > > > peptide bond in amber99 and “N3” is used in Lys side chain. That > > > is why I didn't use backbone peptide. > > > > > > > > > > > > > > > N3 is used in a quaternary amine. N is used in an amide. Atom types are > > related to the chemical functional group they are *now* in, not what they > > were before a notional peptide condensation. You have an amide, and the > > nitrogen in it cannot be protonated. I said that in an email a fortnight > > ago. Use normal peptide parameters. > > > > > > > > > > > > > > > > > > > > > > > > [atoms] and [bonds] section for LYQ > > > and GLQ in topol.top > > > > > > > > > > > > > > > > > > [ atoms ] > > > > > > > > > ; nr type resnr residue atom > > > cgnr charge mass typeBchargeB massB > > > > > > > > >750 amber99_34 48LYQ N > > > 748-0.4157 14.01 ; qtot -5.416 > > > > > > > > >751 amber99_17 48LYQ H > > > 749 0.2719 1.008 ; qtot -5.144 > > > > > > > > >752 amber99_11 48LYQ CA > > > 750 -0.07206 12.01 ; qtot -5.216 > > > > > > > > >753 amber99_19 48LYQ HA > > > 751 0.0994 1.008 ; qtot -5.116 > > > > > > > > >754 amber99_11 48LYQ CB > > > 752 -0.04845 12.01 ; qtot -5.165 > > > > > > > > >755 amber99_18 48LYQHB1 > > > 753 0.034 1.008 ; qtot -5.131 > > > > > > > > >756 amber99_18 48LYQHB2 > > > 754 0.034 1.008 ; qtot -5.097 > > > > > > > > >757 amber99_11 48LYQ CG > > > 7550.06612 12.01 ; qtot -5.031 > > > > > > > > >758 amber99_18 48LYQHG1 > > > 7560.01041 1.008 ; qtot -5.02 > > > > > > > > >759 amber99_18 48LYQHG2 > > > 7570.01041 1.008 ; qtot -5.01 > > > > > > > > >760 amber99_11 48LYQ CD > > > 758 -0.03768 12.01 ; qtot -5.048 > > > > > > > > >761 amber99_18 48LYQHD1 > > > 7590.01155 1.008 ; qtot -5.036 > > > > > > > > >762 amber99_18 48LYQHD2 > > > 7600.01155 1.008 ; qtot -5.025 > > > > > > > > >763 amber99_11 48LYQ CE > > > 7610.32604 12.01 ; qtot -4.699 > > > > > > > > >764 amber99_28 48LYQHE1 > > > 762 -0.03358 1.008 ; qtot -4.732 > > > > > > > > >765 amber99_28 48LYQHE2 > > > 763 -0.03358 1.008 ; qtot -4.766 > > > > > > > > >766 amber99_39 48LYQ NZ > > > 764 -1.03581 14.01 ; qtot -5.801 > > > > > > > > >767 amber99_17 48LYQHZ1 > > > 7650.38604 1.008 ; qtot -5.415 > > > > > > > > >768 amber99_17 48LYQHZ2 > > > 7660.38604 1.008 ; qtot -5.029 > > > > > > > > > > > > > > > Atom 766 is bound to two carbon atoms and two hydrogen atoms. There is no > > such thing as a quaternary amide nitrogen, and certainly AMBER does not > > have parameters for it. > > > > > > > > > > > > > > > > > > > > > > >769 amber99_2 48LYQ C > > > 767 0.5973 12.01 ; qtot -4.432 > > > > > > > > >770 amber99_41 48LYQ O > > > 768-0.5679 16 ; qtot -5 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 2440 amber99_34152GLQ N > > > 2438-0.4157 14.01 ; qtot -12.42 > > > > > > > > > 2441 amber99_17152GLQ H > > > 2439 0.2719 1.008 ; qtot -12.14 > > > > > > > > > 2442 amber99
Re: [gmx-users] isopeptide bond
Dear Mark, Thank you for your help! Now it works! I made MD without errors. I changed N3 to N, add one additional [angletype] to .itp (HP CT N) and removed one of HZ1 from Lys that participate in isopeptide bond; made appropriate changes in .atp, .hdp, .rtp and specbond.dat. 2011/3/14 Mark Abraham > > > On 14/03/11, *Yulian Gavrilov * wrote: > > Dear, Mark > > You asking about this (?): > > According to ffamber99.atp: > > amber99_34 14.01000 ; N sp2 nitrogen in amide groups > > amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) > > If I don't mix, “N” is used in peptide bond in amber99 and “N3” is used > in Lys side chain. That is why I didn't use backbone peptide. > > > N3 is used in a quaternary amine. N is used in an amide. Atom types are > related to the chemical functional group they are *now* in, not what they > were before a notional peptide condensation. You have an amide, and the > nitrogen in it cannot be protonated. I said that in an email a fortnight > ago. Use normal peptide parameters. > > > *[atoms] and [bonds] section for LYQ and GLQ in topol.top * > > [ atoms ] > > ; nr type resnr residue atom cgnr charge mass typeB chargeB massB > > 750 amber99_34 48 LYQ N 748 -0.4157 14.01 ; qtot -5.416 > > 751 amber99_17 48 LYQ H 749 0.2719 1.008 ; qtot -5.144 > > 752 amber99_11 48 LYQ CA 750 -0.07206 12.01 ; qtot -5.216 > > 753 amber99_19 48 LYQ HA 751 0.0994 1.008 ; qtot -5.116 > > 754 amber99_11 48 LYQ CB 752 -0.04845 12.01 ; qtot -5.165 > > 755 amber99_18 48 LYQ HB1 753 0.034 1.008 ; qtot -5.131 > > 756 amber99_18 48 LYQ HB2 754 0.034 1.008 ; qtot -5.097 > > 757 amber99_11 48 LYQ CG 755 0.06612 12.01 ; qtot -5.031 > > 758 amber99_18 48 LYQ HG1 756 0.01041 1.008 ; qtot -5.02 > > 759 amber99_18 48 LYQ HG2 757 0.01041 1.008 ; qtot -5.01 > > 760 amber99_11 48 LYQ CD 758 -0.03768 12.01 ; qtot -5.048 > > 761 amber99_18 48 LYQ HD1 759 0.01155 1.008 ; qtot -5.036 > > 762 amber99_18 48 LYQ HD2 760 0.01155 1.008 ; qtot -5.025 > > 763 amber99_11 48 LYQ CE 761 0.32604 12.01 ; qtot -4.699 > > 764 amber99_28 48 LYQ HE1 762 -0.03358 1.008 ; qtot -4.732 > > 765 amber99_28 48 LYQ HE2 763 -0.03358 1.008 ; qtot -4.766 > > 766 amber99_39 48 LYQ NZ 764 -1.03581 14.01 ; qtot -5.801 > > 767 amber99_17 48 LYQ HZ1 765 0.38604 1.008 ; qtot -5.415 > > 768 amber99_17 48 LYQ HZ2 766 0.38604 1.008 ; qtot -5.029 > > > Atom 766 is bound to two carbon atoms and two hydrogen atoms. There is no > such thing as a quaternary amide nitrogen, and certainly AMBER does not have > parameters for it. > > > 769 amber99_2 48 LYQ C 767 0.5973 12.01 ; qtot -4.432 > > 770 amber99_41 48 LYQ O 768 -0.5679 16 ; qtot -5 > > > > 2440 amber99_34 152 GLQ N 2438 -0.4157 14.01 ; qtot -12.42 > > 2441 amber99_17 152 GLQ H 2439 0.2719 1.008 ; qtot -12.14 > > 2442 amber99_11 152 GLQ CA 2440 -0.0252 12.01 ; qtot -12.17 > > 2443 amber99_19 152 GLQ HA1 2441 0.0698 1.008 ; qtot -12.1 > > 2444 amber99_19 152 GLQ HA2 2442 0.0698 1.008 ; qtot -12.03 > > 2445 amber99_2 152 GLQ C 2443 0.5973 12.01 ; qtot -11.43 > > 2446 amber99_41 152 GLQ O 2444 -0.5679 16 ; qtot -12 > > > > [ bonds ] > > ; ai aj funct c0 c1 c2 c3 > > 750 751 1 > > 750 752 1 > > 752 753 1 > > 752 754 1 > > 752 769 1 > > 754 755 1 > > 754 756 1 > > 754 757 1 > > 757 758 1 > > 757 759 1 > > 757 760 1 > > 760 761 1 > > 760 762 1 > > 760 763 1 > > 763 764 1 > > 763 765 1 > > 763 766 1 > > 766 767 1 > > 766 768 1 > > 766 2445 1 > > > OK, you have the N-C bond for the peptide link. > > > 769 770 1 > > 769 771 1 > > > > 2440 2441 1 > > 2440 2442 1 > > 2442 2443 1 > > 2442 2444 1 > > 2442 2445 1 > > 2445 2446 1 > > > Does 2445 make any other bonds? If not, how did you handle the chain > termination? > > Mark > -- > 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 > -- Sincerely, Yulian Gavrilov -- 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
