[gmx-users] how modify the forcefield amino acid definitions for non-naturally occuring amino acids?
Dear Gmx users, I had been using Gromacs for couple of years and always found these forums quite helpful. Right now again I have another question to ask that I was not able to figure out yet myself and reading previous posts. I need to the ffG53a6 forcefield to be able to recognize the non-standard amino acid like AZE (Azetidine-2-carboxylic acid) which closely resembles Proline, but lacks CH2 group in the ring of the side-group, making the R-group a 4 member ring instead of 5. Thus, this amino acid has very close chemical structure to the Proline which is properly defined in the *.rtp file as below [ PRO ] [ atoms ] N N 0.0 0 CA CH1 0.0 1 CB CH2R 0.0 1 CG CH2R 0.0 2 CD CH2R 0.0 2 C C 0.450 3 O O -0.450 3 [ bonds ] NCAgb_21 NCDgb_21 CACBgb_27 CA Cgb_27 CBCGgb_27 CGCDgb_27 C Ogb_5 C+Ngb_10 [ angles ] ; aiajak gromos type -C NCA ga_31 -C NCD ga_31 CA NCD ga_21 NCACB ga_13 NCA C ga_13 CBCA C ga_13 CACBCG ga_13 CBCGCD ga_13 NCDCG ga_13 CA C O ga_30 CA C+N ga_19 O C+N ga_33 [ impropers ] ; aiajakal gromos type N-CCACD gi_1 CA N CCB gi_2 CCA+N O gi_1 [ dihedrals ] ; aiajakal gromos type -CA-C NCA gd_14 -C NCA C gd_39 CA NCDCG gd_39 NCACBCG gd_34 NCA C+N gd_40 CACBCGCD gd_34 CBCGCD N gd_34 The question is how can I derive from this Proline definition topology the corresponding topology for AZE? The problem is that I do know how to interpret the each column such as the gromos definition column gd_14, etc, as well as other columns. Where can I get information or tutorials about this important issue on how to create own topology files? Maybe someone can explain those columns in easy terms? What are corresponding atoms referred by atom names in the final structure as the there is not ASCI diagram of those as I've seen in AMBER tutorials? Also I am interested in knowing on how the topology files are created from scratch? Any help will be greatly appreciated. Kirill -- 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] Is TRO defined correctly in the ffG43a1p forcefield file?
Dear all, I am trying to run simulation with phosphorylated Threonine (TRO) and I found lot's of info about this issue reading previous posts which explained on how to patch the force-field files and define this modified amino acid. After looking at the community forcefield offered here http://www.gromacs.org/Downloads/User_contributions/Force_fields After exploring those files what calls my attention is that in the *.hdb file that describes which atoms are protonated is seems to have an issue that I wanted to double-check with the rest of the members. It seems to me that the CH3 group is not protonated in the phosphotyrosine (TRO) as shown below Extracted from *.hdp file THR 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA TPO 1 1 1 H N -C CA ...but where is the 2nd line??? Why THR has 2 lines why the TRO having the PO3 group has only one line? Can somebody explain this? Kirill -- 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: how modify the forcefield amino acid definitions for non-naturally occuring amino acids?
Thank you Justin for your prompt reply, as usual :) With the last 2 lines of my previous post, I was referring on how to build *.itp files for completely new molecules (say lipids such as DMPC, DMPE or glutathione) that are not defined in the forcefield. I.e. how to derive dihedral angle code, force constant, etc. so that this new molecules could be used in the simulation. I.e. how to build your own *.itp and *.top files. Or better said, how the parameters for already defined molecules in the forcefield, such as amino-acids and ions were created? Where can we get more information about this ins and outs of building your own topologies? Maybe there are some good references that you can refer me? -- 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] Depth of penetration of DMPC lipid bilayer. How?
Dear gromacs pros, I need to calculate depth of DMPC bilayer penetration by my 14 aa long peptide. I'm not sure how to do it, but I have tried g_dist program and calculated distance between DMPC and peptide groups for every frame of simulation. Is that correct way of doing it or maybe there is a better way? I've got xvg file. First column is time and second is distance in Amstrongs? 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/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] Which membrane result is more reliable?
Hi Justin, Sorry I forgot the attachment. Can you see if these files are ok in terms of sequences and more or less accurately represent both DMPC and DMPE? they were built in Teilman lab I believe DMPE: http://sites.google.com/site/kbessonov/dmpe.itp?attredirects=0d=1 DMPC: http://sites.google.com/site/kbessonov/dmpc.itp?attredirects=0d=1 (for some reason attachements do not go through mailing server) I was trying to understand causes of helix unwinding after 100ns was due to: higher packing density 50 vs 67 A^2/lipid (I've used membrane boxes before protein insertion on top, just to roughly estimate). Could the +/- 15 A^2/lipid error cause this effect of instability? ---tried to analyze edr files using g_energy and total energy option, thinking to get potential energy of the system and conclude stability: DMPC membrane with 62613 atoms (including water and peptide) Energy Average RMSD Fluct. Drift Tot-Drift --- Total Energy-891474 kJ/mol 1132.811131.48 -0.00114556 -190.135 T-Protein 309.844 25.330725.3304 -2.37026e-06 -0.393404 DMPE membrane with 30416 atoms (including also water and peptide) Total Energy: Statistics over 10001 steps [ 0. thru 20.0156 ps ], 1 data sets All averages are exact over 10001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Total Energy-477439 kJ/mol839.231790.016 -0.0049046-980.92 T-Protein_DMPC_DMPE 309.657 3.27193.27189 -9.55346e-08 -0.0191069 Is it OK to multiply DMPE total energy ( -477439 kJ/mol ) by factor of 2 to correct for atom differences between the membranes or it doesn't make sense? I expect DMPE membrane to have slightly higher total energy due to closer packing.please advise. --I have used GridMAT, very cool program, but my results for DMPC membrane were averaging around 80 A^2/lipid, I guess during simulation lipids drift so the density drops (area per lipid increases) ... What else can I do to make sure that my DMPE result is not bogus (maybe increase are per lipid parameter and rerun the system again?) and what other analysis tools can I run on my two membrane systems to compare them. Also where can I get more detailed information on g_energy, since menu options are abbreviated and are not 100% clear? 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/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] Re: Which membrane result is more reliable?
Sorry I've just noted that once of the messages made it to the forum, sorry for repetition. ___ 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] Which membrane result is more reliable?
DMPE.itp file as attached [ moleculetype ] ; Name nrexcl DMPE 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 H 1DMPE H1 0 0.4000 1.0080; qtot:0.36 2 H 1DMPE H2 0 0.4000 1.0080; qtot:0.72 3 H 1DMPE H3 0 0.4000 1.0008; qtot:1.08 4 LNL 1DMPE N4 0-0.5000 14.0067 ; qtot:0.76 5 LH2 1DMPE C5 0 0.3000 14.0270; qtot:1.0 6 LC2 1DMPE C6 1 0.4000 14.0270; qtot:1.0 7 LOS 1DMPE O7 1-0.800 15.9994; qtot:0.54 8 LP1DMPE P8 1 1.700 30.9738; qtot:2.3 9 LOM 1DMPE O9 1-0.800 15.9994; qtot:1.5 10 LOM 1DMPE O10 1-0.800 15.9994; qtot:0.7 11 LOS 1DMPE O11 1-0.700 15.9994; qtot:0 12 LC2 1DMPE C12 2 0.400 14.0270; qtot:0.08 13 LH1 1DMPE C13 2 0.300 13.0190; qtot:0.52 14 LOS 1DMPE O14 2-0.700 15.9994; qtot:-0.14 15 LC 1DMPE C15 2 0.7000 12.0110; qtot:0.56 16 LO 1DMPE O16 2-0.700 15.9994; qtot:0.0 17 LP2 1DMPE C17 3 0.0 14.0270; qtot: 18 LP2 1DMPE C18 4 014.0270; qtot: 19 LP2 1DMPE C19 5 014.0270; qtot: 20 LP2 1DMPE C20 6 014.0270; qtot: 21 LP2 1DMPE C21 7 014.0270; qtot: 22 LP2 1DMPE C22 8 014.0270; qtot: 23 LP2 1DMPE C23 9 014.0270; qtot: 24 LP2 1DMPE C24 10 014.0270; qtot: 25 LP2 1DMPE C25 11 014.0270; qtot: 26 LP2 1DMPE C26 12 014.0270; qtot: 27 LP2 1DMPE C27 13 014.0270; qtot: 28 LP2 1DMPE C28 14 014.0270; qtot: 29 LP3 1DMPE C29 15 015.0350; qtot: 30 LC2 1DMPE C32 16 0.5014.0270; qtot: 31 LOS 1DMPE O33 16 -0.7015.9994; qtot: 32 LC 1DMPE C34 16 0.8012.0110; qtot: 33 LO 1DMPE O35 16 -0.6015.9994; qtot: 34 LP2 1DMPE C36 17 014.0270; qtot: 35 LP2 1DMPE C37 18 014.0270; qtot: 36 LP2 1DMPE C38 19 014.0270; qtot: 37 LP2 1DMPE C39 20 014.0270; qtot: 38 LP2 1DMPE C40 21 014.0270; qtot: 39 LP2 1DMPE C41 22 014.0270; qtot: 40 LP2 1DMPE C42 23 014.0270; qtot: 41 LP2 1DMPE C43 24 014.0270; qtot: 42 LP2 1DMPE C44 25 014.0270; qtot: 43 LP2 1DMPE C45 26 014.0270; qtot: 44 LP2 1DMPE C46 27 014.0270; qtot: 45 LP2 1DMPE C47 28 014.0270; qtot: 46 LP3 1DMPE C48 29 015.0350; tail: [ bonds ] ; aiaj funct 1 4 1 0.1E+00 0.37450E+06 2 4 1 0.1E+00 0.37450E+06 3 4 1 0.1E+00 0.37450E+06 4 5 1 0.14700E+00 0.37660E+06 5 6 1 0.15300E+00 0.33470E+06 6 7 1 0.14300E+00 0.25100E+06 7 8 1 0.16100E+00 0.25100E+06 8 9 1 0.14800E+00 0.37660E+06 8 10 1 0.14800E+00 0.37660E+06 8 11 1 0.16100E+00 0.25100E+06 11 12 1 0.14300E+00 0.25100E+06 12 13 1 0.15300E+00 0.33470E+06 13 14 1 0.14350E+00 0.25100E+06 13 30 1 0.15300E+00 0.33470E+06 14 15 1 0.13600E+00 0.37660E+06 15 16 1 0.12300E+00 0.50210E+06 15 17 1 0.15300E+00 0.33470E+06 17 18 1 0.15300E+00 0.33470E+06 18 19 1 0.15300E+00 0.33470E+06 19 20
[gmx-users] Which membrane result is more reliable?
Hello Justin, You helped me before, and I am grateful for that. So basically my summer research had ended up with the following results: I have included my *.ipt files this message is long. *My question: 1)why once simulation is giving me stable aplha-helix and other is not if membranes are similar and conditions kept constant. * 2) Which result to use, most probale. Does lipid density might of affected the stability? -200ns Simulation of the same peptide in the DMPC only box and in DMPC/DMPE box [1:1 ratio] but results are different and I want to ask why as this data will go as part of the paper. *System:* peptide that is placed on TOP of the membrane, interacting with lipids (no inserted into the membrane, but floating on top) and above there are water molecules * DMPC membrane simulation - STABLE Peptide Helix, no uncoiling:* - 248 DMPC molecules -Box 9.03 x 9.03 x 10.15 as found at the bottom of gro file (I think this dimensions are nm units?) - Threfore I calculated that Area per Lipid is only: 2facesx90.3^2 A^2/248DMPC = 65.75 A^2/lipid which is low - When I was using InflatGro(which I modified to be much more friendly and accepts 2 lipids) to check the lipid density the values were: ___ Input *.gro file to shrink or expand:dmpc.gro Enter membrane re-scaling factor (default=0.95):*1* Enter Lipid#1 name (e.g. DMPC):DMPC Enter Lipid#2 name (e.g. DMPE) otherwise ENTER: For spacial overlap estimation between lipids... Please enter distance cutoff value between lipids in A(default = 14):14 Output file name(e.g.'inflated.gro'):rm.gro Gridsize for area per lipid calculations in A(default = 5):5 TOTAL Area per protein: 1.5 nm^2 or 150.00 A^2 *TOTAL Area per lipid: 0.67 nm^2 or 67.26 A^2* -- why different from prev. calculation, slightly smaller? Area per protein, upper half: 0.000 nm^2or 0.000 A^2 Area per lipid, upper leaflet : 0.632 nm^2 or 63.210 A^2 Area per protein, lower half: 1.50 nm^2or 150.00 A^2 Area per lipid, lower leaflet : 0.73 nm^2 or 73.43 A^2 ___ Total Energy: Statistics over 82987501 steps [ 109970.0078 thru 275945. ps ], 1 data sets All averages are exact over 82987501 steps Energy Average RMSD Fluct. Drift Tot-Drift --- *Total Energy-891474 *kJ/mol 1132.811131.48 -0.00114556 -190.135 T-Protein 309.844 25.330725.3304 -2.37026e-06 -0.393404 *DMPE/DMPC membrane simulation - Becomes UNSTABLE after 100ns simulation time * - 93 DMPC and 93 DMPE molecules -Density: 2faces*68.2*68.2 / 186 lipids = 50 A^2/lipid - InflateGro results: _ TOTAL Area per protein: 0 nm^2 or 0.00 A^2 *TOTAL Area per lipid: 0.49 nm^2 or 48.52 A^2* again smaller? Area per protein, upper half: 0.000 nm^2or 0.000 A^2 Area per lipid, upper leaflet : 0.485 nm^2 or 48.517 A^2 Area per protein, lower half: 0.00 nm^2or 0.00 A^2 Area per lipid, lower leaflet : 0.49 nm^2 or 48.52 A^2 Writing Area per lipid... Done! ___ DMPC: has 46 atoms and DMPE: has 46 atoms Total Energy: Statistics over 10001 steps [ 0. thru 20.0156 ps ], 1 data sets All averages are exact over 10001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- *Total Energy-477439 kJ/mol * 839.231790.016 -0.0049046-980.92 T-Protein_DMPC_DMPE 309.657 3.27193.27189 -9.55346e-08 -0.0191069 I used the same *.mdp file *I used following dmpe.ipt and dmpc files * attached that to my 1st impression are identical ___ 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] do_dssp question
I have used do_dssp program to analyze secondary structure during simulation of DMPC/DMPE. But I am not clear on installation of dssp. The program seems to work, I have set all the environmental variables so that dssp binary is seen in /home/DSSP directory, but I am not sure if I need to download the database of dssp files from the internet to make this program work. There are 14 residues in your selected group Opening library file /usr/local/gromacs/share/gromacs/top/ss.map trn version: GMX_trn_file (single precision) Reading frame 0 time 52.000 Back Off! I just backed up ddoSxMLN to ./#ddoSxMLN.1# Last frame 0 time 52.000 100% And I get ss.xps file that when I open it in image viewer is just a blue line. How should I properly setup the program and whether it will give me %alpha helicity over the course of the trajectory, 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/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] Peptide drifting and non-natural amino acids
I was giving today my poster presentation and one of profs from my department was very critical on the fact that my peptide is drifting or moving along the DMPC bilayer. Watch video of 100ns simulation here: He said that is unprobable, I want to know if this is some kind of artifact (i.e. system is diffusing). I had DMPC molecules displaying artifacts, so I converted trajectory with trjconv -pbc mol -ur compact Another question: I want to start simulation of a pepetide that has non-natural amino acid (Azetidine -2 - carbpxylic acid, AZE in short). The only structural difference is that proline has 5 membered ring and AZE only 4. Therefore I was wondering if it is at all possible to simulate that kind of peptide, since I expect complains from grompp about amino acid name, AZE not being in its database. Please advise on how to approach this problem Thanks ___ 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] RE: Peptide drifting and non-natural amino acids
Sorry the link: You see that peptide is moving from right to the left of the box http://www.youtube.com/watch?v=_6e4Rfl6Yrc ___ 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] Peptide - DMPC membrane simulations - Unstable system
Hi Justin, So after struggling through ... I have confirmed that the error was due to Gromacs version incompatibility. Now my simulation is past problematic step and continues running without any error. Also I am following your advice and also doing the same simulation but with two equilibration steps as per your tutorial. The pressure equilibration step had generated 7Gb *.trr file, is this normal for 10ns equilibration? I have used mdp files from tutorial too. I have question about COM (center of mass) parameters. What happens if we forget about them and do not do the grouping of Solvent+Na+ + Cl- and Protein+DMPC, what could happen? The layer will slide past each other, or what? And one more question about your tutuorial and my previous experiences: Also when I was running InflateGRO my box size incread 4x, so it became huge, 25x25x25, and after compression by 0.95 factor is was around 22x22x22. Therefore I have used the box that we had in the lab already. Is this normal, because visiaully lipids are too spaced out and that's why water enters btwn them when you solvate, to the poin that I wrote C++ program that removes water from lipid bilayer. ___ 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] Peptide - DMPC membrane simulations - Unstable system
I think I have not arrived to complete solution of my problem yet, but I think the cause of early LINCS warnings were version incompatibility. I am now trying to run simulation on the server that has only 4.0.5 Gromacs, will see if that helps and whether I will warnings in the middle of simulations. I have tried PR simulation on peptide and it failed even earlier (after 10,000 steps), maybe this indicates version issues, as I would assume PR simulations are more stable as they does not allow peptide to enter DMPC layer So after 20 ns of simulation on the server with Gromacs 4.0 I've started to get errors and LINCS warnings and simulation collapsed, I have resumed simualtion as per oldwiki instructions, but again it soon failed. After looking at the trajectory with VMD I see that the peptide sinks into DMPC and one phenyl ring flips out (Phe residue). Maybe due to local constrains and being surrounded by DMPC the errors start coming up. I am not sure. I will do the movie and post it on youtube as ato show you what is going on. Why does the system fails after 10,578,600 steps? Is there way to ignore LINCS warnings and make simulation run anyways, if yes how? I was not sure what to try next. Try to do several EM steps to get system to 500 kJ/mol, right now it is at 800 kJ/mol? Or try to do longer equilibration steps by restraining protein using posre.itp file included in topology as per your tutorial? Thanks for your time. ___ 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] Peptide - DMPC membrane simulations - Unstable system
Hello gain Justin, Now I figured out that the problem was in gromacs version 4.0. So peptide in water works no problem. I have used trjconv -pbc mol -ur compact and it solved the artifact problem. Thanks a lot! Now I have started simulation on 96 CPU's for 1000ns total run time. But after 1 day simulation the system crashed or exploded with the following error: [First time it failed because of some problems with the server, and then I have resumed the run using tpbconv -s DMPCRun1000ns.tpr -f 1000nsDMPCA141Run_part1.trr -extend 10 -o DMPCRun100nspart2.tpr] vol 0.78 imb F 2% pme/F 2.15 step 10578400, will finish Sat Aug 29 07:23:01 2009 vol 0.77 imb F 3% pme/F 2.15 step 10578500, will finish Sat Aug 29 07:28:32 2009 Step 10578599, time 21157.2 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.299801, max 6.073617 (between atoms 9449 and 9450) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 9451 9468 93.60.1530 0.1293 0.1530 Fatal error: 15 particles communicated to PME node 6 are more than a cell length out of the domain decomposition cell of their charge group I am attaching my mdp files used to to EM and MDrun here: EM: http://kbessonov.googlepages.com/em_lipid.mdp MD: http://kbessonov.googlepages.com/mdonly_1000ns.mdp I was wondering why my system fails. and what can I do to avoid it? I was thinking maybe to run several times EM on the system, maybe it will help? What bugs me is that it fails really late in simulation. I have not seen trajectory file yet. ___ 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] Peptide - DMPC membrane simulations - Unstable system
Hello again, Thanks for quick replies! I've tried to see what happens if I put peptide in water and sure enough it failed (uses gromacs 4.0). But when I run it on machine that I have created the *.tpr file it runs no problem already 5000 steps and the machine uses gromacs 4.0.5. How could it be possible, after all the Gromacs versions are very similar. To solavate I have used genbox -cp protein.gro -cs DMPCbox(bilayer with water ontop) -box [dimensions] - I have attached images, also if the didn't come through I have included lincs to them: http://kbessonov.googlepages.com/DMPC_cage.gif http://kbessonov.googlepages.com/A141_simulSys.png http://kbessonov.googlepages.com/A141inDMPC.GIF After running simulation for couple of hours I have discovered that DMPC molecules are flying apart, showing as some rays in a form of a cage as you see form the DMPC pic. What can I do to prevent this artifact, is there trjconv command to ma ke corrections so I do not see this strange artifact? ___ 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] Re: number of coordinates in coordinate file does not match topology
I have written a C++ program that can do it for you in 5 minutes. If you interested I can send you link to executable. It counts #of solute molecules and #Na+ and Cl- ions plus DMPC, but I can adjust it so it can count any number of molecules, I need to know how many atoms per molecule and it reads gro file now, I do not work with pdb, but if needed I can do it form pdb too. ___ 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] Peptide - DMPC membrane simulations - Unstable system
Hi guys, I am trying to start simulation on lipid - peptide system, but receive LINCS warnings of angles rotating more than 30 deg which means that my system is unstable. I have tried to do mdrun on the DMPC box itself and had no problems. Once I insert my peptide, the problems starts. I have run Energy MInimization with LIncs order or 4 and Lincs iterations 8, but still could not bring system to 200 kJ/mol Fmax. Received the following message. Converged to machine precision, but not to the requested precision Fmax 100 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Back Off! I just backed up sys_EM_ready.gro to ./#sys_EM_ready.gro.2# Steepest Descents converged to machine precision in 499 steps, but did not reach the requested Fmax 100. Potential Energy = -1.2830664e+06 Maximum force = 3.4162991e+03 on atom 2 Norm of force = 3.2566280e+01 Now I am trying to just to do EM (energ. minim) on my 14 aa peptide, in water box just to see if it will work. My questions: -How to position peptide into existing lipid box (apart form using editconf -rotate parameter). I have tried VMD and did it visually, but new coordingates were not saved? -How I can improve on EM, what kinda setting in mdp file can I use to that system converges even after 10,000 steps? -How to prevent clashes, maybe there are some settings to try with genbox -cp -cs command? Thanks ___ 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] Re: Extend water layer along negative Z-direction
You can try to position your system in Z direction using: editconf -princ (and bunch of other normal parameters) Also you can use -rotate parameter to align your system along any axis Hope it helps ___ 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] Peptide - DMPC membrane simulations - Unstable system
Thank you Justin, I have tried to just solvate the peptide in water box using genbox command and spc216 water Then I have used the Energy Min mdp file form your tutorial (I have been folowing your tutorial for couple of days, the difference is that I want to put my segment on top of the membrane between the head groups of phospholipids). The DMPC box is stable, but I have trouble with 14aa peptide. It seems that is is unstable, I have made NH2 and COOO termini, maybe this is the problem? The results of EM for peptide in water: Step= 786, Dmax= 6.3e-03 nm, Epot= -1.37798e+06 Fmax= 7.60491e+02, atom= 67 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 787 steps Potential Energy = -1.3779814e+06 Maximum force = 7.6049121e+02 on atom 67 Norm of force = 1.8584177e+01 Then I run mdrun using mdp file that we use usually in our lab, and system crashed with LINCS warnings after 75 steps. But when I use the mdp file that is in EM section of your tutorial and change integrator = md. The peptide in water system is running without any warnings up till step 300. step 300, Warning: 1-4 interaction between 54 and 59 at distance 2.342 which is larger than the 1-4 table size 2.200 nm What settings would you recommend for MD runs in mdp files? Could you explain from your tutorial: How to Reduce the charges on the H atoms (all the way to zero, if necessary) Restore the charges before continuing And how Add [ exclusions ] within the topology between H and phosphate O atoms Remove the exclusions before continuing Thanks ___ 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
