Re: [gmx-users] simulation with ligand at the active site
onetwo wrote: Hello Users, I have a query regarding simulation with the ligand. In my protein there are two ligands, one of them (coenzyme) is from the crystal data, and other I have docked at the active site, while docking it is showing good interaction with all the active site residues very well. I used GROMOS96 43a1 force field, and got the topology file made from prodrg beta, using GROMOS 96.1 for both the ligands. PRODRG produces notoriously bad topologies. See, for instance: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips while doing equilibration I did, brendenson coupling on like ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 and in MD simulation also ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 There could be some debate about these settings, and I do not know the best way to handle temperature coupling. It seems to me that if you have a ligand (or multiple) bound to a protein, the interactions between the protein and ligand(s) will be tightly coupled, such that you shouldn't lump the ligands into the Non-Protein group, which in this case likely comprises solvent. Maybe someone with more experience in these types of simulations can share some insight. But after 1ns equibiration, one of the ligand (the one which I docked) is going away from the active site and then I ran it for 4 ns further, it has gone more far from the cavity. Following is the link to the snapshot of the ligand at different time. https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402 I want to ask if the change in the position of ligand is justified with the parameters i have taken or it if i have done something wrong? Without providing the actual topology(ies) of the ligand(s) and a complete .mdp file, it is hard to say. But if you're using PRODRG output, I would suspect that it would be the culprit. -Justin Thanks and Regards http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? -- 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] rigid tetrahedral molecule
On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) I think it's seven coupled triangles, but that's not a relevant way to think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 9 independent descriptors of relative atomic positions, so 9 constraints. You were trying 10 and 5. Because those constraints form triangles, you may need to take care with LINCS to get a stable simulation. Read up on the details here, I don't remember them. In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. Forget about SETTLE - it was just an example to illustrate that this is not easy to do right. There's a specialised algorithm for rigid water (with three coupled bond constraints) because it is fiddly to get such things right (and fast). Mark *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 11:14:34 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and opls_1015 . Initially I tried to put contsraint along all bonds ( i.e among F atoms as well ). But, grompp provides warning that number of constraint is more than number of degrees of freedom. So, I reduced number of constraints by only putting constraint among B and F. But, it did not work either. Sure, you need as many constraints as http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29 You should also do your homework about using LINCS and coupled triangles of constraints, as I suggested last time. Mark Here is the .itp file I wrote for rigid BF4 . It will be great if someone can point me what I am doing wrong. [ moleculetype ] ; molname nrexcl BF4 3 [ atoms ] #ifdef _FF_OPLS 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 #endif [ constraints ] 1 2 1 0.146 1 3 1 0.146 1 4 1 0.146 1 5 1 0.146 ; 2 3 1 0.238 ; 2 4 1 0.238 ; 2 5 1 0.238 ; 3 4 1 0.238 ; 3 5 1 0.238 ; 4 5 1 0.238 [ exclusions ] 1 2 34 5 2 1 34 5 3 1 24 5 4 1 23 5 5 1 23 4 *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 8:39:23 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 11:25 AM, Justin A. Lemkul wrote: Sanku M wrote: Hi, I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed. I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule. I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ? Can someone suggest the best wayout ? Constraints should do
Re: [gmx-users] simulation with ligand at the active site
On 4/28/2011 3:21 PM, onetwo wrote: Hello Users, I have a query regarding simulation with the ligand. In my protein there are two ligands, one of them (coenzyme) is from the crystal data, and other I have docked at the active site, while docking it is showing good interaction with all the active site residues very well. I used GROMOS96 43a1 force field, and got the topology file made from prodrg beta, using GROMOS 96.1 for both the ligands. while doing equilibration I did, brendenson coupling on like ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale You used V-rescale (per the command), not Berendsen (per the comment). However, that's not a problem. tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 and in MD simulation also ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 But after 1ns equibiration, one of the ligand (the one which I docked) is going away from the active site and then I ran it for 4 ns further, it has gone more far from the cavity. Following is the link to the snapshot of the ligand at different time. https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402 I want to ask if the change in the position of ligand is justified with the parameters i have taken or it if i have done something wrong? It is well known (and published) that PRODRG can produce garbage charges. Perhaps you have evidence of that here. If you expect your ligand to stay bound, it may make more sense to T-couple it with the protein, using a custom index group, then to couple it with solvent. However, I'd look at my charges first. 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
Re: [gmx-users] Docking
Dear Aldo Thank you for your reply Mark's notes and yours were very useful. Best mohsen On Wed, Apr 27, 2011 at 6:46 PM, Aldo Segura asegurac...@yahoo.com.mxwrote: Before making a MD simulation you should try to explore different ways to analyze your docking results. For example, performing the same experiment with different docking programs and scoring functions (“consensus scoring”) and compare the results, is there consistency between them?. Now, if docking results are not successful in terms of prior knowledge of your system (is there structural information of your system? articles?), you could select several of the complex predicted by the docking program and make a MD simulation and free energy calculation, compare the results for each complex and verify if the results improve according to what you expected. However, as mentioned by Mark, simulations and calculations like these involve much computational resources and time. Best regards, Aldo ** *=== Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com =* --- El *mié 27-abr-11, Mark Abraham mark.abra...@anu.edu.au* escribió: De: Mark Abraham mark.abra...@anu.edu.au Asunto: Re: [gmx-users] Docking A: Discussion list for GROMACS users gmx-users@gromacs.org Fecha: miércoles, 27 de abril de 2011, 5:27 On 4/27/2011 7:52 PM, mohsen ramezanpour wrote: Dear Mark Thank you for your reply.yes,you are right. Regarding question 2: I have a pdf file from Docking Server for sertraline-SERT example.Suppose this is a good docked state. In the other hand,I did what I explained in section 1 for sertraline and SERT.(by pymol and ...) Now, I want to check if I have docked sertraline to SERT correctly or not( by comparing with Docking server's one) How can I do that? Comparing MD-docked structures and otherwise-docked structures is easy - look at the RMS deviation of atom positions, to start with. However, a small or large deviation is not evidence that either docked structure bears any relationship to what happens in vivo. Do you have any suggestion for doing docking by gromacs? for example pulling code, MD , or SMD? People use these kinds of methods for good reasons. Time spent reading up on how and why is time well spent. Mark Thanks in advance On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham mark.abra...@anu.edu.auhttp://mc/compose?to=mark.abra...@anu.edu.au wrote: On 4/27/2011 7:05 PM, mohsen ramezanpour wrote: Dear Users I read so many emails to mailing list, there were important notes about docking but I couldn't extract a general result. Please let me know: 1-Can we dock a ligand to it's protein's binding pocket with Pymol and Gromacs as following? first:locating ligand outside and close to binding site manually in pymol and saving complex.pdb second:doing all steps for generating complex.top and complex.gro as Enzyme-Drug tutorial third:running md (with out any pull code and constraint),in the other words,full flexible system. I think drug can move freely and according to it's interaction with binding site can be attracted by binding site. reside for a distance time and then will come out of pocket. Am I right? In principle, yes, but it is wildly unlikely that you have a system that can bind and unbind reliably in the 100ns simulation range that you might be able to afford to run, and if you did happen to have one, what would you have learned? I know what discussed in mainling list about deffinition of Docking. 2-I have some docked files by Docking Server for some of my drug-protein's complexes. now,I want to obtain them by doing MD in the above proccess.if I was successful then try to do that for other drugs which I don't have any docked pdb for them. How can I fit a trajectory with a typical pdb file? I don't understand what you are asking. Mark -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=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.orghttp://mc/compose?to=gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -Sigue archivo adjunto- -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=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
[gmx-users] R: Md continuation with cpt
Dear Justin, thank you for your precious help. Yes, the problem is what you say and what I was suspecting too (but I was not sure, that's why I was searching for a confirmation of my suspects from more expert people). The problem however is present in the NVT-NPT junction. My .mdp settings were NVT: tinit = 0 init_step = 0 nsteps = 1 dt = 0.002 NPT tinit = 0 init_step = 2 (instead of 1) nsteps = 5 dt = 0.002 That's why I had a last NPT step of 7 instead of 6, and that's why I set init_step = 7 in the production MD. What you are saying also explains the anomalous behaviour of the xvg file created from the .edr file, in which only few points were saved, therefore the graphs created with xmgrace contain only 7 values (at 140, 200, 300 400, 5140, 10140, 15140 ps). I always set nstep identical to the last step of the previous equilibration MD because I understood that it was necessary to do it to obtain an exact continuation, there is no other special reason. Since you are saying that this is no (longer?) necessary (I'm currently using Gromacs 4.0.7 on this machine), I'm very happy to set always nsteps = 0, to avoid future mistakes. In the meantime, what I have to do? I had a look at the .xtc files with gmxcheck and apparently all is fine, with no error messages, also the trajectory seems to be coherent with my expectations. I run g_rms and g_gyrate and the behaviour of the systems appears normal (apart from the fact that the system is not stabilized yet, so I have to continue the trajectory). I can provide you (offlist) the .xvg graphs, if you want. Based on these data, what do you suggest to do? Do you think that the simulation could be considered formally correct (i.e. this is only a problem of erroneous writing of .edr file) or do I have to repeat (AARRH) the whole simulation? I saw in the manual that the option -rerun of mdrun command allows to recalculate forces and energies from a trajectory file, do you think that I can use it to obtain a new .edr file? Thank you as usual for your invaluable help Anna PS: i'm asking just another suggestion, to the gmx-users administrators. I receive the mails from gmx-users list in form of digest. How can I do to reply to messages extracted from the digest in order to create a continuous thread in the archive? At present, I'm making a reply to the digest message in order to keep the gmx-users list updated, but it seems to me that the messages are stored as separated. -- Message: 1 Date: Wed, 27 Apr 2011 11:18:51 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Md continuation with cpt To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4db833db.4050...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: Dear gmx-users, since I'm sending my simulations to a system with a queue with a wallclock time of 24 h, I necessarily have to simulate small parts of my simulation, that I stick together at the end with trjconv. To continue my simulations, I'm using the .cpt file. Here my settings concerning the number of steps, dt etc. Since I started the full MD after 20 ps NVT and 100 ps NPT I set the mdp file as: integrator = md dt = 0.002 nsteps = 250 (total 5 ns - the max time compatible with the wallclock time) init_step = 7 (the last step after NVT+NPT) Is it? 120 ps/0.002 ps = 6 steps. snip Opened 1R3Afull20ns.edr as double precision energy file frame: 0 (index 0), t:140.000 Based on this output, frame 0 corresponds to a time of 140 ps, as set by your init_step * dt. Reading energy frame 2 time 300.000 Timesteps at t=200 don't match (60, 100) It looks like the setting for nstenergy is causing frames to be written at integral multiples of 100 ps, rather than init_step + nstenergy. So you have frame 0 at 140 ps, frame 1 at 200 ps, then 100-ps intervals until... Reading energy frame 50 time 5100.000 Timesteps at t=5100 don't match (100, 40) etc. Timesteps at t=5140 don't match (40, 60) Timesteps at t=5200 don't match (60, 100) Reading energy frame100 time 1.000 Timesteps at t=10100 don't match (100, 40) Timesteps at t=10140 don't match (40, 60) Timesteps at t=10200 don't match (60, 100) Reading energy frame150 time 14900.000 Timesteps at t=15100 don't match (100, 40) Timesteps at t=15140 don't match (40, 60) Timesteps at t=15200 don't match (60, 100) Last energy frame read 198 time 19600.000 All of these mismatches seem to agree with the above theory. The difference is always 40 or 60, the remainder of some break between your value determined by init_step and initial time of 140 ps. Found 199 frames. gcq#131: Royale With Cheese (Pulp Fiction) I don't understand why there are so many mismatches
[gmx-users] Fwd: Fwd: Need some assistence
Could someone assist me seeing as i am only a beginner at molecular dynamics i have generated models using modeller software and selected the best model based on DOPE GA341 and Prosa now i have performed energy minimisations using gromacs software. I further energy refined the structures using gromacs. The steps were as follows: For in vacuo minimisation Steepest descent 1000 steps and conjugated gradient of 3000 steps. Could you perhaps just check the parameter files (st.mdp and con.mdp) and commands (commands) used to ensure the correct procedures and selections were made in order to ensure my peace of mind. The command files contain outputs I also performed minimisations using periodic boundary conditions adding ions and solvated the system this also were performed using similar conditions as in the in vacuo minimisation. These files are also attached parameter files (em.mdp and con1.mdp) and commands (commands1). Thank you very much i appreciate any and all advice given by you. Best Regards Ruben Cloete South Africa ; Conjugate gradient with morse potential in vacuo ; User Kerrigan (236) ; ; Input file ; cpp = /usr/bin/cpp constraints = none integrator = cg nsteps = 3000 ; ; Energy minimising stuff ; emtol= 100 emstep = 0.01 nstcgsteep = 1000 nstcomm = 1 ns_type = grid morse= yes coulombtype = Shift vdw_type = Shift rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r= 6.0 Tcoupl = no Pcoupl = no gen_vel = no ; Steepest Descents in vacuo ; User Kerrigan (236) ; ; Input file ; cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 1000 ; ; Energy minimising stuff ; emtol= 1000.0 emstep = 0.01 nstcomm = 1 ns_type = grid morse= no coulombtype = Shift vdw_type = Shift rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r= 6.0 Tcoupl = no Pcoupl = no gen_vel = no In vacuo energy minimisation pdb2gmx -f cmk.pdb -o cmk.gro -p cmk.top -ignh use Gromos 96.1 (43A2) 1 editconf -bt cubic -f cmk.gro -d 1.0 editconf -f out.gro -o cmk_ctr.gro -center 3.89025 3.89025 3.89025 steepest descents (1000 steps) grompp -f st.mdp -c cmk_ctr.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_vacuum.pdb -g em.log -e em.edr Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 1000 writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 5 steps Potential Energy = -4.9777656e+03 Maximum force = 5.3928821e+02 on atom 682 Norm of force = 1.3912250e+02 conjugated gradient (3000 steps) grompp -f con.mdp -c cmk_ctr.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_vacuum.pdb -g em.log -e em.edr Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e+02 Number of steps= 3000 F-max = 2.80126e+04 on atom 1512 F-Norm= 7.57882e+03 writing lowest energy coordinates. Back Off! I just backed up cmk_EM_vacuum.pdb to ./#cmk_EM_vacuum.pdb.1# Polak-Ribiere Conjugate Gradients converged to Fmax 100 in 68 steps Potential Energy = -4.9642773e+03 Maximum force = 9.7731384e+01 on atom 1636 Norm of force = 2.3101681e+01 ion wet energy minimisation pdb2gmx -f cmk.pdb -o cmk.gro -p cmk.top -ignh use Gromos 96.1 (43A2) 1 editconf -bt cubic -f cmk.gro -d 1.0 7.78050 7.78050 7.78050 editconf -f out.gro -o cmk_ctr.gro -center 3.89025 3.89025 3.89025 genbox -cp cmk_ctr.gro -cs spc216.gro -o cmk-b4em.gro -p cmk.top Output configuration contains 46207 atoms in 14923 residues Volume : 471.002 (nm^3) Density: 1045.51 (g/l) Number of SOL molecules: 14693 grompp -f em.mdp -c cmk-b4em.gro -p cmk.top -o cmk_em.tpr NOTE 1 [file cmk.top, line 13399]: System has non-zero total charge: -5.98e+00 genion -s cmk_em.tpr -o cmk_ion.gro -pname NA+ -np 6 -g cmk_ion.log Select a group: 12 Steepest descents (1000 steps) I must run it again grompp -f em.mdp -c cmk_ion.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_ionwet.pdb -g em.log -e em.edr Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps= 1000 ruben@rubennb:~/Desktop/EM_latest/Rv1712_ionwet$ ps PID TTY
[gmx-users] Metal surfaces
Hello, does anybody have an idea if there are availbale PDB files which represent metal surfaces for transition state metals, to be used for MD? BW S -- 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] rigid tetrahedral molecule
Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of constraints ), we would have 4 bonds ( 1-2,1-3,1-4,1-5 ) and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5 , 4-1-5 )at 109.45 degrees , thus total ( 4+6)=10 descriptors . In that case, the simulation goes fine . But, then wonder, why, for constraints, we can put only 9 descriptors . Also, I have tried all possible combination to get 9 constraints, but , in each case, gromacs crashes. However, defining 4 bonds and 6 angles using high force-constant lets the simulation go fine. So, on a second thought, I wonder whether defining 9 bond-constraints to get a stable tetrahedral molecule is at all possible. Do I need to go for some sort of compromise, where 4 bonds ( 1-2,1-3,1-4,1-5 ) are defined as constraints and 6 angles with high force-constant are defined to maintain tetrahedral nature ? I am not sure what should be the best possible 9 constraints . 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, April 28, 2011 1:00:42 AM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule .I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) I think it's seven coupled triangles, but that's not a relevant way to think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 9 independent descriptors of relative atomic positions, so 9 constraints. You were trying 10 and 5. Because those constraints form triangles, you may need to take care with LINCS to get a stable simulation. Read up on the details here, I don't remember them. In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. Forget about SETTLE - it was just an example to illustrate that this is not easy to do right. There's a specialised algorithm for rigid water (with three coupled bond constraints) because it is fiddly to get such things right (and fast). Mark From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, April 27, 2011 11:14:34 PM Subject: Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and opls_1015 . Initially I tried to put contsraint along all bonds ( i.e among F atoms as well ). But, grompp provides warning that number of constraint is more than number of degrees of freedom. So, I reduced number of constraints by only putting constraint among B and F. But, it did not work either. Sure, you need as many constraints as
[gmx-users] RE: Metal surfaces (Sergio Manzetti)
Hi,
That's unlikely, but maybe the following publications can help you to build the
surface:
@Article{Iori2008,
author = Iori, F and Corni, S,
title = {Including image charge effects in the molecular dynamics simulations
of molecules on metal surfaces},
journal = J Comput Chem,
year = 2008,
volume = 29,
pages = 1656-1666
}
@Article{Iori2009,
author = Iori, F and Di Felice, R and Molinari, E and Corni, S,
title = {{G}ol{P}: {A}n atomistic force-field to describe the interaction of
proteins with {A}u(111) surfaces in water},
journal = J Comput Chem,
year = 2009,
volume = 30,
pages = 1465-1476
}
@article{Kalcher2009,
Author = {Kalcher, I. and Horinek, D. and Netz, R. R. and Dzubiella, J.},
Title = {{Ion specific correlations in bulk and at biointerfaces}},
Journal = {JOURNAL OF PHYSICS-CONDENSED MATTER},
Year = {{2009}},
Volume = {{21}},
Article-Number = {{424108}}
}
Ran Friedman
Biträdande Lektor (Assistant Professor)
Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden
Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.fried...@lnu.se
http://lnu.se/ccbg
Hello, does anybody have an idea if there are availbale PDB files which
represent metal surfaces for transition state metals, to be used for MD?
BW
S
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Re: [gmx-users] RE: Metal surfaces (Sergio Manzetti)
Thank you
On Thu, Apr 28, 2011 at 6:26 PM, Ran Friedman ran.fried...@lnu.se wrote:
Hi,
That's unlikely, but maybe the following publications can help you to build
the surface:
@Article{Iori2008,
author = Iori, F and Corni, S,
title = {Including image charge effects in the molecular dynamics
simulations of molecules on metal surfaces},
journal = J Comput Chem,
year = 2008,
volume = 29,
pages = 1656-1666
}
@Article{Iori2009,
author = Iori, F and Di Felice, R and Molinari, E and Corni, S,
title = {{G}ol{P}: {A}n atomistic force-field to describe the interaction
of proteins with {A}u(111) surfaces in water},
journal = J Comput Chem,
year = 2009,
volume = 30,
pages = 1465-1476
}
@article{Kalcher2009,
Author = {Kalcher, I. and Horinek, D. and Netz, R. R. and Dzubiella, J.},
Title = {{Ion specific correlations in bulk and at biointerfaces}},
Journal = {JOURNAL OF PHYSICS-CONDENSED MATTER},
Year = {{2009}},
Volume = {{21}},
Article-Number = {{424108}}
}
Ran Friedman
Biträdande Lektor (Assistant Professor)
Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden
Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.fried...@lnu.se
http://lnu.se/ccbg
Hello, does anybody have an idea if there are availbale PDB files which
represent metal surfaces for transition state metals, to be used for MD?
BW
S
--
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] rigid tetrahedral molecule
On 4/28/2011 7:07 PM, Sanku M wrote: Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of constraints ), we would have 4 bonds ( 1-2,1-3,1-4,1-5 ) and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5 , 4-1-5 )at 109.45 degrees , thus total ( 4+6)=10 descriptors . Different things happen in each case. A redundant but consistent bonded interaction adds (at most) a small contribution to the energies and forces. Consider what the effect of a suitably-constructed H-H-C angle function of a methylene in an equilibrium configuration would be... nothing significant. However, an implementation of coupled constraints so that they are all mutually satisifed in few iterations is hard enough without having to cope with redundancy also. In that case, the simulation goes fine . But, then wonder, why, for constraints, we can put only 9 descriptors . Also, I have tried all possible combination to get 9 constraints, but , in each case, gromacs crashes. However, defining 4 bonds and 6 angles using high force-constant lets the simulation go fine. So, on a second thought, I wonder whether defining 9 bond-constraints to get a stable tetrahedral molecule is at all possible. So you need to read the LINCS and/or SHAKE literature :-) You say these other codes can do rigid-body simulations, so there must be literature on how to do it. Do I need to go for some sort of compromise, where 4 bonds ( 1-2,1-3,1-4,1-5 ) are defined as constraints and 6 angles with high force-constant are defined to maintain tetrahedral nature ? Maybe. I am not sure what should be the best possible 9 constraints . Don't know. I would start trying four B-F bonds and five F-F bonds, but it shouldn't matter. Mark 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thu, April 28, 2011 1:00:42 AM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) I think it's seven coupled triangles, but that's not a relevant way to think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 9 independent descriptors of relative atomic positions, so 9 constraints. You were trying 10 and 5. Because those constraints form triangles, you may need to take care with LINCS to get a stable simulation. Read up on the details here, I don't remember them. In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. Forget about SETTLE - it was just an example to illustrate that this is not easy to do right. There's a specialised algorithm for rigid water (with three coupled bond constraints) because it is fiddly to get such things right (and fast). Mark *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 11:14:34 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and
Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote: Thanks Mark for your comment. But, as far as degrees of freedom is concerned, if there is a tetrahedral molecule as I shown below with atom #1 ( B) being center of the tetrahedron , if we had defined the molecules in terms of bonds and angles ( in stead of constraints ), we would have 4 bonds ( 1-2,1-3,1-4,1-5 ) and 6 angles ( 2-1-3,2-1-4,2-1-5,3-1-4,3-1-5 , 4-1-5 )at 109.45 degrees , thus total ( 4+6)=10 descriptors . In that case, the simulation goes fine . But, then wonder, why, for constraints, we can put only 9 descriptors . Also, I have tried all possible combination to get 9 constraints, but , in each case, gromacs crashes. However, defining 4 bonds and 6 angles using high force-constant lets the simulation go fine. So, on a second thought, I wonder whether defining 9 bond-constraints to get a stable tetrahedral molecule is at all possible. Do I need to go for some sort of compromise, where 4 bonds ( 1-2,1-3,1-4,1-5 ) are defined as constraints and 6 angles with high force-constant are defined to maintain tetrahedral nature ? I am not sure what should be the best possible 9 constraints . For an example, see the CHCL3 definition in the Gromos96 53A6 force field. -Justin 1 opls_1014 1BF4B 1 0.8276 2 opls_1015 1BF4F1 1 -0.4569 3 opls_1015 1BF4F2 1 -0.4569 4 opls_1015 1BF4F3 1 -0.4569 5 opls_1015 1BF4F4 1 -0.4569 *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thu, April 28, 2011 1:00:42 AM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 3:49 PM, Sanku M wrote: I went through the LINCS manual . But, I am still struggling with coming up with the idea of putting correct constraint to maintain the rigidity of tetrahedral molecule . I seem to understand from your suggestion that the tetrahedral can be seen as a combination of 4 coupled triangles.( or am I still wrong about it ?) I think it's seven coupled triangles, but that's not a relevant way to think about it. You have 5 atoms, so 3N-6 means 9 degrees of freedom, so you need 9 independent descriptors of relative atomic positions, so 9 constraints. You were trying 10 and 5. Because those constraints form triangles, you may need to take care with LINCS to get a stable simulation. Read up on the details here, I don't remember them. In that case, am I supposed to use multiple settle to keep the molecule in a tetrahedral fashion ? I am sorry but if you can explain it in bit more details, I might get the point. Forget about SETTLE - it was just an example to illustrate that this is not easy to do right. There's a specialised algorithm for rigid water (with three coupled bond constraints) because it is fiddly to get such things right (and fast). Mark *From:* Mark Abraham mark.abra...@anu.edu.au *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wed, April 27, 2011 11:14:34 PM *Subject:* Re: [gmx-users] rigid tetrahedral molecule On 4/28/2011 1:54 PM, Sanku M wrote: Hi, I tried to keep the geometry of the BF4 fixed by using constraints using lincs. But , unfortunately, my simulation is crashing immediately and if I try minimization with only 2 molecules, it provides a lot of LINCS warning and generate a lot of step*.pdb file . If I try to visualize the minimized snapshot in VMD, it looks like all the distances I tried to constrain decreased drastically. Finally, trying MD run with this minimized configuration results in crashing due to bad contacts. I am sure I am doing something wrong and it might be that my itp file is wrong . So any help will be highly appreciated. Here is the details of what I did. The geometry of the molecule is tetrahedral with B at the center and 4 F atoms is surrounding it in a tetrahedral manner. I first generated a itp file for BF4 which is shown below: I first got the LJ parameters and charges for B and F atom and put them in ffoplsnb.itp file as new atom types opls_1014 and opls_1015 . Initially I tried to put contsraint along all bonds ( i.e among F atoms as well ). But, grompp provides warning that number of constraint is more than number of degrees of freedom. So, I reduced number of constraints by only putting constraint among B and F. But, it did not work either. Sure, you need as many constraints as http://en.wikipedia.org/wiki/Degrees_of_freedom_%28physics_and_chemistry%29 You should also do your homework about using LINCS and coupled triangles of constraints, as I suggested last time. Mark Here is the .itp file I wrote for rigid BF4 . It will be great if someone can point me what I am doing wrong. [
Re: [gmx-users] Fwd: Fwd: Need some assistence
On 4/28/2011 6:10 PM, Ruben Cloete wrote: Could someone assist me seeing as i am only a beginner at molecular dynamics i have generated models using modeller software and selected the best model based on DOPE GA341 and Prosa now i have performed energy minimisations using gromacs software. I further energy refined the structures using gromacs. The steps were as follows: For in vacuo minimisation Steepest descent 1000 steps and conjugated gradient of 3000 steps. Could you perhaps just check the parameter files (st.mdp and con.mdp) and commands (commands) used to ensure the correct procedures and selections were made in order to ensure my peace of mind. The command files contain outputs I also performed minimisations using periodic boundary conditions adding ions and solvated the system this also were performed using similar conditions as in the in vacuo minimisation. These files are also attached parameter files (em.mdp and con1.mdp) and commands (commands1). Thank you very much i appreciate any and all advice given by you. Seems fine - but you should look up in section 7.3 of the manual what everything does and satisfy yourself that your choices make sense with what you know about molecular simulations. Read the relevant sections earlier in the manual and do all the tutorial material and textbook reading you can find, even if it's off-topic for you. 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
Re: [gmx-users] R: Md continuation with cpt
On 4/28/2011 5:47 PM, Anna Marabotti wrote: Dear Justin, thank you for your precious help. Yes, the problem is what you say and what I was suspecting too (but I was not sure, that's why I was searching for a confirmation of my suspects from more expert people). The problem however is present in the NVT-NPT junction. My .mdp settings were NVT: tinit = 0 init_step = 0 nsteps = 1 dt = 0.002 NPT tinit = 0 init_step = 2 (instead of 1) nsteps = 5 dt = 0.002 That's why I had a last NPT step of 7 instead of 6, and that's why I set init_step = 7 in the production MD. What you are saying also explains the anomalous behaviour of the xvg file created from the .edr file, in which only few points were saved, therefore the graphs created with xmgrace contain only 7 values (at 140, 200, 300 400, 5140, 10140, 15140 ps). I always set nstep identical to the last step of the previous equilibration MD because I understood that it was necessary to do it to obtain an exact continuation, there is no other special reason. The label on the step number has nothing to do with the physics. Instructions for restarts preserving simulation ensembles are on the website. IIRC init_step refers to the label given to the step whose time is tinit (see manual 7.3.3), and haphazardly changing only one of them might lead to such problems. Since you are saying that this is no (longer?) necessary (I'm currently using Gromacs 4.0.7 on this machine), I'm very happy to set always nsteps = 0, to avoid future mistakes. Do that. In the meantime, what I have to do? I had a look at the .xtc files with gmxcheck and apparently all is fine, with no error messages, also the trajectory seems to be coherent with my expectations. I run g_rms and g_gyrate and the behaviour of the systems appears normal (apart from the fact that the system is not stabilized yet, so I have to continue the trajectory). I can provide you (offlist) the .xvg graphs, if you want. Based on these data, what do you suggest to do? Do you think that the simulation could be considered formally correct (i.e. this is only a problem of erroneous writing of .edr file) or do I have to repeat (AARRH) the whole simulation? I saw in the manual that the option -rerun of mdrun command allows to recalculate forces and energies from a trajectory file, do you think that I can use it to obtain a new .edr file? If it's just a problem of labelling the frames, then trjcat and eneconv have -settime to deal with these kinds of scenarios. 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] pdb2gmx with input topology
Dear Gromacs users, I wish to convert PDB files to gromacs format while specifying the topology; however, in the pdb2gmx program, a .top file can only be an output, not an input. The need arises as I have an NMR PDB structure (including hydrogens) which I rather violently perturb into multiple PDB structures using some non-gromacs means. When I convert those structures to .gro using pdb2gmx, sometimes the protonation state of Histidine is guessed incorrectly by the program (the hydrogen moves between HD1 and HE2). Does anybody have a suggestion what can I do? I need the process to be automatic and so can't use the interactive -his option. Thanks, Ehud. -- 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] pdb2gmx with input topology
Ehud Schreiber wrote: Dear Gromacs users, I wish to convert PDB files to gromacs format while specifying the topology; however, in the pdb2gmx program, a .top file can only be an output, not an input. The need arises as I have an NMR PDB structure (including hydrogens) which I rather violently perturb into multiple PDB structures using some non-gromacs means. When I convert those structures to .gro using pdb2gmx, sometimes the protonation state of Histidine is guessed incorrectly by the program (the hydrogen moves between HD1 and HE2). If the atoms are properly named, I don't see how this is possible, unless you're using the -ignh option. If the atomic coordinates are severely skewed, you should at least get a warning about long bonds. Does anybody have a suggestion what can I do? I need the process to be automatic and so can’t use the interactive -his option. So is the .top the same in all cases, and you're just altering coordinates? If so, pdb2gmx is not necessary at all. Just use the .top you want in conjunction with any of the .pdb files. But perhaps I've missed the point. There is definitely no way to input a .top into pdb2gmx since its principal function is to produce such a file. -Justin Thanks, Ehud. -- 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] pdb2gmx with input topology
On 4/28/2011 10:25 PM, Justin A. Lemkul wrote: Ehud Schreiber wrote: Dear Gromacs users, I wish to convert PDB files to gromacs format while specifying the topology; That is not the role of pdb2gmx. pdb2gmx generates a topology that matches a configuration (which could be in one of many file formats), and (as a side effect) produces a cleaned up version of that configuration (which again could be in one of many file formats). If you already have your configuration and a .top file that has one or more [moleculetype] sections that match the molecules present in your configuration, you do not need pdb2gmx. Perhaps this will help you reconsider whether your workflow is appropriate. Mark however, in the pdb2gmx program, a .top file can only be an output, not an input. The need arises as I have an NMR PDB structure (including hydrogens) which I rather violently perturb into multiple PDB structures using some non-gromacs means. When I convert those structures to .gro using pdb2gmx, sometimes the protonation state of Histidine is guessed incorrectly by the program (the hydrogen moves between HD1 and HE2). If the atoms are properly named, I don't see how this is possible, unless you're using the -ignh option. If the atomic coordinates are severely skewed, you should at least get a warning about long bonds. Does anybody have a suggestion what can I do? I need the process to be automatic and so can’t use the interactive -his option. So is the .top the same in all cases, and you're just altering coordinates? If so, pdb2gmx is not necessary at all. Just use the .top you want in conjunction with any of the .pdb files. But perhaps I've missed the point. There is definitely no way to input a .top into pdb2gmx since its principal function is to produce such a file. -Justin Thanks, Ehud. -- 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] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field
Dear gmx users, Recently I have parametrized a new force field for glycolipid molecules based on the GLYCAM parameters. I would like to use it with the AMBER99SB-ILDN force field in gromacs for simulations of peptides and glycolipds. As you know GLYCAM uses two different values for fudgeLJ and fudgeQQ (e.g. set to 1.0) instead of 0.5 and 0.8333 values. So it is possible to define two different fudgeLJ and fudgeQQ values in GROMACS (as in AMBER11, for example) for the micelle and the peptides. I have found an old response (2007) in the list archive for a old version of gromacs http://lists.gromacs.org/pipermail/gmx-users/2007-February/025907.html Since this response have been posted 4 years ago, i am not sure that this approach can be also use with the current version of gromacs ? Thank you in advance for your response Stephane -- 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] simulation with ligand at the active site
Previously, something like happened to me, the solution that worked for me was to use acpype (code.google.com/p/acpype) and Amber FF. In this way, you could rule out problems related to the prodrg parameters. Best regards, Aldo === Aldo Segura-Cabrera Laboratorio de Bioinformática Centro de Biotecnología Genómica Instituto Politécnico Nacional Blvd. Del Maestro esquina Elías Piña, 88710 Reynosa, Tamaulipas, México. (899)9243627 ext. 87747 e-mail: asegu...@ipn.mx; aldoseg...@gmail.com = --- El jue 28-abr-11, Justin A. Lemkul jalem...@vt.edu escribió: De: Justin A. Lemkul jalem...@vt.edu Asunto: Re: [gmx-users] simulation with ligand at the active site A: Discussion list for GROMACS users gmx-users@gromacs.org Fecha: jueves, 28 de abril de 2011, 1:02 onetwo wrote: Hello Users, I have a query regarding simulation with the ligand. In my protein there are two ligands, one of them (coenzyme) is from the crystal data, and other I have docked at the active site, while docking it is showing good interaction with all the active site residues very well. I used GROMOS96 43a1 force field, and got the topology file made from prodrg beta, using GROMOS 96.1 for both the ligands. PRODRG produces notoriously bad topologies. See, for instance: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips while doing equilibration I did, brendenson coupling on like ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 and in MD simulation also ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 There could be some debate about these settings, and I do not know the best way to handle temperature coupling. It seems to me that if you have a ligand (or multiple) bound to a protein, the interactions between the protein and ligand(s) will be tightly coupled, such that you shouldn't lump the ligands into the Non-Protein group, which in this case likely comprises solvent. Maybe someone with more experience in these types of simulations can share some insight. But after 1ns equibiration, one of the ligand (the one which I docked) is going away from the active site and then I ran it for 4 ns further, it has gone more far from the cavity. Following is the link to the snapshot of the ligand at different time. https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402 I want to ask if the change in the position of ligand is justified with the parameters i have taken or it if i have done something wrong? Without providing the actual topology(ies) of the ligand(s) and a complete .mdp file, it is hard to say. But if you're using PRODRG output, I would suspect that it would be the culprit. -Justin Thanks and Regards http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? -- 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 -- 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] Benchmarking gromacs over large number of cores
Hi, I'm not really a Gromacs user, but I'm currently benchmarking Gromacs 4.5.4 on a large cluster. It seems that my communication (PME) is really high and gromacs keeps complaining for more PME nodes : Average load imbalance: 113.6 % Part of the total run time spent waiting due to load imbalance: 3.3 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % Y 9 % Z 9 % Average PME mesh/force load: 3.288 Part of the total run time spent waiting due to PP/PME imbalance: 32.6 % NOTE: 32.6 % performance was lost because the PME nodes had more work to do than the PP nodes. You might want to increase the number of PME nodes or increase the cut-off and the grid spacing. I can't modify the original dataset as I only have the TPR file. I switched from dlb yes - dlb auto since it seems to have trouble with more than 6000 / 8000 cores. I tried to add -gcom parameter. This speedup the computation. This parameter is not really explained in the Gromacs documentation. Could you give me some advice on how I could use it ? Best regards, Bruno Monnet -- 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] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field
Stephane: The problem is the coulombic 1-4 interactions. There is not (and never has been as far as I can tell) a way to get different 1-4 coulombic scaling for different pairs. There is a trick that works when combining one ff that uses fudgeQQ 1.0 and another that uses fudgeQQ 0.5: http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049428.html . This trick can be applied to obtain micelle fudgeLJ 1.0 and fudgeQQ 1.0 and, simultaneously, peptide fudgeLJ 0.5 and fudgeQQ = 5/6 (close but not exactly 0.8333 due to rounding) as follows: 1. set the fudgeLJ to 1.0 and fudgeQQ to 0.16 2. calculate the micelle [ pairtypes ] interactions according to the combination rules of the ff and then divide the values by 6. You can include these values/6 in the pairtypes section or directly in the pairs section. 3. calculate the protein [ pairtypes ] interactions according to the combination rules of the ff and then divide the values by 10. You can include these values/12 in the pairtypes section or directly in the pairs section. 4. Include all of the micelle [ pairs ] 6 times and all of the peptide [ pairs ] 5 times in their respective topologies The energy should be nearly correct. The only problems will be (a) different internal rounding due to different order of operations (this will be very small and will get even smaller in double precision) and (b) based on the fact that 0.8333 is not exactly 5/6 in the first place (you're stuck with this one). You will need to test that I got the values correctly above. To do that, you can compute the pair energy of micelle and protein systems individually using the standard ff files and then again using the modified version that is detailed above and that should work for both. If you use this, an appropriate reference would be as an extension of the half-epsilon double-pairlist method: Biophys J. 2010 Mar 3;98(5):784-792. An Iris-Like Mechanism of Pore Dilation in the CorA Magnesium Transport System. Chakrabarti N, Neale C, Payandeh J, Pai EF, Pomès R. Chris. -- original message -- Dear gmx users, Recently I have parametrized a new force field for glycolipid molecules based on the GLYCAM parameters. I would like to use it with the AMBER99SB-ILDN force field in gromacs for simulations of peptides and glycolipds. As you know GLYCAM uses two different values for fudgeLJ and fudgeQQ (e.g. set to 1.0) instead of 0.5 and 0.8333 values. So it is possible to define two different fudgeLJ and fudgeQQ values in GROMACS (as in AMBER11, for example) for the micelle and the peptides. I have found an old response (2007) in the list archive for a old version of gromacs http://lists.gromacs.org/pipermail/gmx-users/2007-February/025907.html Since this response have been posted 4 years ago, i am not sure that this approach can be also use with the current version of gromacs ? Thank you in advance for your response Stephane -- 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] R: Md continuation with cpt
Dear Mark, thank you very much for your hint. It's a relief to know that I haven't to redo the simulation! From now on I will set init_step = 0 for my simulations. Anna -- Message: 3 Date: Thu, 28 Apr 2011 20:56:00 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] R: Md continuation with cpt To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4db947c0.90...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/28/2011 5:47 PM, Anna Marabotti wrote: Dear Justin, thank you for your precious help. Yes, the problem is what you say and what I was suspecting too (but I was not sure, that's why I was searching for a confirmation of my suspects from more expert people). The problem however is present in the NVT-NPT junction. My .mdp settings were NVT: tinit = 0 init_step = 0 nsteps = 1 dt = 0.002 NPT tinit = 0 init_step = 2 (instead of 1) nsteps = 5 dt = 0.002 That's why I had a last NPT step of 7 instead of 6, and that's why I set init_step = 7 in the production MD. What you are saying also explains the anomalous behaviour of the xvg file created from the .edr file, in which only few points were saved, therefore the graphs created with xmgrace contain only 7 values (at 140, 200, 300 400, 5140, 10140, 15140 ps). I always set nstep identical to the last step of the previous equilibration MD because I understood that it was necessary to do it to obtain an exact continuation, there is no other special reason. The label on the step number has nothing to do with the physics. Instructions for restarts preserving simulation ensembles are on the website. IIRC init_step refers to the label given to the step whose time is tinit (see manual 7.3.3), and haphazardly changing only one of them might lead to such problems. Since you are saying that this is no (longer?) necessary (I'm currently using Gromacs 4.0.7 on this machine), I'm very happy to set always nsteps = 0, to avoid future mistakes. Do that. In the meantime, what I have to do? I had a look at the .xtc files with gmxcheck and apparently all is fine, with no error messages, also the trajectory seems to be coherent with my expectations. I run g_rms and g_gyrate and the behaviour of the systems appears normal (apart from the fact that the system is not stabilized yet, so I have to continue the trajectory). I can provide you (offlist) the .xvg graphs, if you want. Based on these data, what do you suggest to do? Do you think that the simulation could be considered formally correct (i.e. this is only a problem of erroneous writing of .edr file) or do I have to repeat (AARRH) the whole simulation? I saw in the manual that the option -rerun of mdrun command allows to recalculate forces and energies from a trajectory file, do you think that I can use it to obtain a new .edr file? If it's just a problem of labelling the frames, then trjcat and eneconv have -settime to deal with these kinds of scenarios. 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] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field
Aargh !! it is not easy :(((, I will try, your trick, Chris. By the way, thank your for pointing the paper. A bientot Stéphane Message: 5 Date: Thu, 28 Apr 2011 10:45:17 -0400 From: chris.ne...@utoronto.ca Subject: [gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field To: gmx-users@gromacs.org Message-ID: 20110428104517.0vv03ebm04wkg...@webmail.utoronto.ca Content-Type: text/plain; charset=ISO-8859-1; DelSp=Yes; format=flowed Stephane: The problem is the coulombic 1-4 interactions. There is not (and never has been as far as I can tell) a way to get different 1-4 coulombic scaling for different pairs. There is a trick that works when combining one ff that uses fudgeQQ 1.0 and another that uses fudgeQQ 0.5: http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049428.html . This trick can be applied to obtain micelle fudgeLJ 1.0 and fudgeQQ 1.0 and, simultaneously, peptide fudgeLJ 0.5 and fudgeQQ = 5/6 (close but not exactly 0.8333 due to rounding) as follows: 1. set the fudgeLJ to 1.0 and fudgeQQ to 0.16 2. calculate the micelle [ pairtypes ] interactions according to the combination rules of the ff and then divide the values by 6. You can include these values/6 in the pairtypes section or directly in the pairs section. 3. calculate the protein [ pairtypes ] interactions according to the combination rules of the ff and then divide the values by 10. You can include these values/12 in the pairtypes section or directly in the pairs section. 4. Include all of the micelle [ pairs ] 6 times and all of the peptide [ pairs ] 5 times in their respective topologies The energy should be nearly correct. The only problems will be (a) different internal rounding due to different order of operations (this will be very small and will get even smaller in double precision) and (b) based on the fact that 0.8333 is not exactly 5/6 in the first place (you're stuck with this one). You will need to test that I got the values correctly above. To do that, you can compute the pair energy of micelle and protein systems individually using the standard ff files and then again using the modified version that is detailed above and that should work for both. If you use this, an appropriate reference would be as an extension of the half-epsilon double-pairlist method: Biophys J. 2010 Mar 3;98(5):784-792. An Iris-Like Mechanism of Pore Dilation in the CorA Magnesium Transport System. Chakrabarti N, Neale C, Payandeh J, Pai EF, Pomhs R. Chris. -- original message -- Dear gmx users, Recently I have parametrized a new force field for glycolipid molecules based on the GLYCAM parameters. I would like to use it with the AMBER99SB-ILDN force field in gromacs for simulations of peptides and glycolipds. As you know GLYCAM uses two different values for fudgeLJ and fudgeQQ (e.g. set to 1.0) instead of 0.5 and 0.8333 values. So it is possible to define two different fudgeLJ and fudgeQQ values in GROMACS (as in AMBER11, for example) for the micelle and the peptides. I have found an old response (2007) in the list archive for a old version of gromacs http://lists.gromacs.org/pipermail/gmx-users/2007-February/025907.html Since this response have been posted 4 years ago, i am not sure that this approach can be also use with the current version of gromacs ? Thank you in advance for your response Stephane -- -- 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! End of gmx-users Digest, Vol 84, Issue 231 ** -- 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] Benchmarking gromacs over large number of cores
how many particles is your system? if the number per domain is too low there is not much you can do about the load imbalance...but it did report only an overall 3.2% overhead for this so... you can modify the PP/PME ratio during mdrun by manually specifying the domain decomposition yourself. so for example since you are off by 33%, try to specify the dd count so you end up with 3x the nodes for PME than you did before... example: set -dd 10 10 10 to use 1000 PP nodes the rest will be PME nodes; you can use a nonsquare matrix just try to minimze the condition number -gcom effectively overrides nstcalenergy, as it tells each node how many steps to run before synchronizing. Usually, mdrun will let you know about excessive wait times for synch but we do not see it here with your system (must be running some really high end infiniband!) -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Bruno Monnet bruno.mon...@hp.com wrote: Hi, I'm not really a Gromacs user, but I'm currently benchmarking Gromacs 4.5.4 on a large cluster. It seems that my communication (PME) is really high and gromacs keeps complaining for more PME nodes : Average load imbalance: 113.6 % Part of the total run time spent waiting due to load imbalance: 3.3 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % Y 9 % Z 9 % Average PME mesh/force load: 3.288 Part of the total run time spent waiting due to PP/PME imbalance: 32.6 % NOTE: 32.6 % performance was lost because the PME nodes had more work to do than the PP nodes. You might want to increase the number of PME nodes or increase the cut-off and the grid spacing. I can't modify the original dataset as I only have the TPR file. I switched from dlb yes - dlb auto since it seems to have trouble with more than 6000 / 8000 cores. I tried to add -gcom parameter. This speedup the computation. This parameter is not really explained in the Gromacs documentation. Could you give me some advice on how I could use it ? Best regards, Bruno Monnet -- 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] ordering components of system using trjorder
Dear gmx-users, I wish to order the components of my system with respect to the polypeptide using trjorder. I want to select my first group as the protein and the second group to be ordered is non-protein (i.e all other components in the system except polypeptide) the command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -o ordered.gro The problem is -na int is required, but the rest of my system contains TIP4P water, methanol, Li ions so the na is different for all non-protein components. Is there a way to override option -na and still get non-protein part of the system ordered with respect to the polypeptide (protein) Thanks, SN -- 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: gmx-users Digest, Vol 84, Issue 217
Hi Ivan If in my system there are some of the other components such SDS surfactant and one of these polarizable models can I use forcefield parameters from PRODRG or not. If no, would you please tell me about the references that I can find some other components in polarizable water model force fields. Thanks alot for your help Regards Saly On Wed, Apr 27, 2011 at 5:29 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: polarizable water models (Mark Abraham) 2. Re: polarizable water models (Ivan Gladich) -- Message: 1 Date: Wed, 27 Apr 2011 22:39:56 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] polarizable water models To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4db80e9c.7010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/27/2011 10:08 PM, saly jackson wrote: Hi Ivan Please do not reply to whole digests with non-descriptive subject lines. It confuses the archives, and alienates people from finding out the topic of your interest, and thus being bothered to give you free help. Please leave only the relevant discussion, and use a useful subject line. In which force field can I find the polarizable water models you said in section b of your reply Have you done your own literature searching first? Then you'd already know what force fields they might have been used with... Mark -- Message: 2 Date: Wed, 27 Apr 2011 15:43:27 +0200 From: Ivan Gladich ivan.glad...@marge.uochb.cas.cz Subject: Re: [gmx-users] polarizable water models To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4db81d7f.70...@marge.uochb.cas.cz Content-Type: text/plain; charset=iso-8859-1 Skipped content of type multipart/alternative-- next part -- ; ; Topology file for SW ; ; Paul van Maaren and David van der Spoel ; Molecular Dynamics Simulations of Water with Novel Shell Model Potentials ; J. Phys. Chem. B. 105 (2618-2626), 2001 ; ; Force constants for the shell are given by: ; ; k = qs^2/(4 pi eps0 alpha) ; However, in the current version of the itp file and software (3.2+) ; force constants are computed in mdrun, and the input is the ; polarizability in nm^3. ; ; Some data: mu (water) = 1.8546 D ( 0.0386116 e nm) ;1/(4 pi eps0 alpha) = 94513.94 ; ; Alpha-X = 1.415 kx = 608069 ; Alpha-Y = 1.528 ky = 563101 ; Alpha-Z = 1.468 kz = 586116 ; ; Alpha = 1.470 k = 585318 ; ; Bonding parameters from (but without cubic term): ; D. M. Ferguson: ; Parametrization and Evaluation of a Flexible Water Model ; J. Comp. Chem. 16(4), 501-511 (1995) ; ; Possible defines that you can put in your topol.top: ; -DANISOTROPIC Select anisotropic polarizibility (isotropic is default). ; -DRIGID Rigid model (flexible is default) ; -DPOSRES Position restrain oxygen atoms ; [ defaults ] LJ Geometric [ atomtypes ] ;namemass charge ptype c6 c12 WO15.99940 0.0 A 0.0 0.0 WH 1.00800 0.0 A 0.0 0.0 WS 0.0 0.0 S 0.0 0.0 WD 0.0 0.0 D 0.0 0.0 [ nonbond_params ] #ifdef RIGID #ifdef ANISOTROPIC WH WH 1 4.0e-5 4.0e-8 WS WO 1 1.0e-6 1.0e-12 WS WH 1 4.0e-5 2.766e-08 WO WO 1 2.0e-3 1.174e-06 #else WH WH 1 4.0e-5 4.0e-8 WS WO 1 1.0e-6 1.0e-12 WS WH 1 4.0e-5 2.769e-08 WO WO 1 2.0e-3 1.176e-06 #endif #else #ifdef ANISOTROPIC WH WH 1 4.0e-5 4.0e-8 WS WO 1 1.0e-6 1.0e-12 WS WH 1 4.0e-5 2.910e-08 WO WO 1 2.0e-3 1.189e-06 #else WH WH 1 4.0e-5 4.0e-8 WS WO 1 1.0e-6 1.0e-12 WS WH 1 4.0e-5 2.937e-08 WO WO 1 2.0e-3 1.187e-06 #endif #endif ;; This is a the 'classical YAW' model, in which we do have the dummy. ;; The shell is attached to the dummy, in this case the gas-phase ;; quadrupole is correct.
[gmx-users] trjorder not working
Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? Thanks, SN -- 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] Benchmarking gromacs over large number of cores
On Thu, Apr 28, 2011 at 10:05 AM, Bruno Monnet bruno.mon...@hp.com wrote: Hi, I'm not really a Gromacs user, but I'm currently benchmarking Gromacs 4.5.4 on a large cluster. It seems that my communication (PME) is really high and gromacs keeps complaining for more PME nodes : Average load imbalance: 113.6 % Part of the total run time spent waiting due to load imbalance: 3.3 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 % Y 9 % Z 9 % Average PME mesh/force load: 3.288 Part of the total run time spent waiting due to PP/PME imbalance: 32.6 % NOTE: 32.6 % performance was lost because the PME nodes had more work to do than the PP nodes. You might want to increase the number of PME nodes or increase the cut-off and the grid spacing. I can't modify the original dataset as I only have the TPR file. I switched from dlb yes - dlb auto since it seems to have trouble with more than 6000 / 8000 cores. You can set the number of PME nodes with -npme. All other nodes are used for the particle-particle computations (PP).There is also a tool called g_tune_pme which optimizes it automatically for you. On that many cores you might see a significant speed-up by using the prerelease version of GROMACS 4.6. You can obtain that from git using the branch threading. It uses threading for the PME nodes. The number of threads used by the PME nodes is set with the environment variable GMX_PME_NTHREADS. The total number of cores should be equal to the number of PP nodes + GMX_PME_NTHREADS * number of PP nodes. Let me know if you try it - I would be interested in feedback. I tried to add -gcom parameter. This speedup the computation. This parameter is not really explained in the Gromacs documentation. Could you give me some advice on how I could use it ? It defines how often e.g. the total energy is computed which is important for pressure and temperature coupling. As long as you don't set it to higher than 10 it shouldn't affect the accuracy significantly. But it does effect it minimally thus you should document that in your results. Roland Best regards, Bruno Monnet -- 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 -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] how to get higher precision values for g_velacc
Dear gmx users, I am using g_velacc to calculate the velocity auto correlation. The output I am getting in .xvg file is much lower precision than I require. Is there a way to get the values in higher precision? Thanks, SN -- 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] vdw cutoff options for opls forcefield
Hi, I was wondering whether someone can comment on what vdw-cutoff scheme will be suitable when using a molecule under OPLS/AA force field . Also, providing some details about what cut-off value one should use will be really helpful. Thanks 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] Turning OFF/ON distance restraints during a simulation
Hi all, Is it possible to turn OFF/ON distance restraints after simulating a system for a certain period of time? If yes, how do I command GMX to do such a job? Thank you James -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- 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] Turning OFF/ON distance restraints during a simulation
On 4/29/2011 9:09 AM, jayant james wrote: Hi all, Is it possible to turn OFF/ON distance restraints after simulating a system for a certain period of time? If yes, how do I command GMX to do such a job? You can do this only by stopping the simulation and re-invoking grompp with the changed conditions. 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
Re: [gmx-users] vdw cutoff options for opls forcefield
On 4/29/2011 8:28 AM, Sanku M wrote: Hi, I was wondering whether someone can comment on what vdw-cutoff scheme will be suitable when using a molecule under OPLS/AA force field . Also, providing some details about what cut-off value one should use will be really helpful. Generally, one should use the cut-off scheme that was used in the parametrization, unless some relevant subsequent work has demonstrated that an alternative scheme works acceptably. So check out the literature - you'll have to read and cite it eventually! One caveat is that there is broad acceptance for using PME electrostatics rather than the plain cut-off schemes with which most of the common force fields were parametrized. As such, one doesn't need to reproduce the Coulomb cut-off, because that cut-off value has a fundamentally different role. You can't reproduce a plain cut-off scheme with PME (and wouldn't want to). 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
Re: [gmx-users] how to get higher precision values for g_velacc
On 4/29/2011 4:48 AM, shivangi nangia wrote: Dear gmx users, I am using g_velacc to calculate the velocity auto correlation. The output I am getting in .xvg file is much lower precision than I require. Is there a way to get the values in higher precision? Depends what you've done so far, but either you need to collect velocity data more often, or in double precision, or both. 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
Re: [gmx-users] trjorder not working
On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. 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
Re: [gmx-users] how to get higher precision values for g_velacc
I want the velocity autocorrelation output in double precision. How can I get that? Thanks, SN --- On Thu, 4/28/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] how to get higher precision values for g_velacc To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, April 28, 2011, 8:21 PM On 4/29/2011 4:48 AM, shivangi nangia wrote: Dear gmx users, I am using g_velacc to calculate the velocity auto correlation. The output I am getting in .xvg file is much lower precision than I require. Is there a way to get the values in higher precision? Depends what you've done so far, but either you need to collect velocity data more often, or in double precision, or both. Mark -- 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 -- 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] how to get higher precision values for g_velacc
On 4/29/2011 10:34 AM, shikha nangia wrote: I want the velocity autocorrelation output in double precision. How can I get that? Install GROMACS in double precision. Depending what the problem is, you might be able to run the double-precision g_velacc on the old data to get more precision, or else you'll need to run your simulation in double-precision to collect data in double precision first. Mark Thanks, SN --- On *Thu, 4/28/11, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] how to get higher precision values for g_velacc To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, April 28, 2011, 8:21 PM On 4/29/2011 4:48 AM, shivangi nangia wrote: Dear gmx users, I am using g_velacc to calculate the velocity auto correlation. The output I am getting in .xvg file is much lower precision than I require. Is there a way to get the values in higher precision? Depends what you've done so far, but either you need to collect velocity data more often, or in double precision, or both. Mark -- gmx-users mailing list gmx-users@gromacs.org /mc/compose?to=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 /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjorder not working
Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. 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 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] trjorder not working
On 4/29/2011 11:29 AM, shivangi nangia wrote: Hello, The manual explaining trjorder says: trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate (with option -z). With distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected molecules will be reordered according to the shortest distance between atom number -da in the molecule and all the atoms in the reference group. *The center of mass of the molecules can be used instead of a reference atom by setting -da to 0* In order to arrange water molecules in accordance with the COM of the polypeptide, I chose -da 0. As it says above, -da refers to an atom or COM of the molecule, not the reference group. This could be worded better in the documentation. Be sure you're choosing the groups you think you are choosing - you not copying relevant parts of your terminal output into emails is making things difficult. Mark Am I wrong? Thanks, SN On Thu, Apr 28, 2011 at 8:29 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 4/29/2011 4:08 AM, shivangi nangia wrote: Hello all, I am trying to order the TIP4P water molecules in my system with respect to the polypeptide in my system. The command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o ordered.gro This runs without any error and ordered.gro is generated with random sequence of water molecules. Just to cross check I calculated the distances between one of atoms of the polypeptide and oxyegn atom of different ordered water molecules. I found, there is no ascendig trend in the distances with respect to the polypeptide as a go down in the ordered.gro file. What could be going wrong? -da 0 has a particular effect - is it appropriate? Did you choose the right groups? You could use the -nshell option to probe what trjorder thinks is going on. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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
