Re: [gmx-users] request
Hi, Define an itp file which has the non-bonded info. Then define a mdp (md parameter file) and also make a structure file (gro). Also you need a topology file (top) which corresponds to the structure file. You will have to do some background work. Manual should be your friend. amit On Sat, Nov 20, 2010 at 11:32 PM, leila separdar separdar.le...@gmail.comwrote: I am beginner with gromacs. I would like to simulate the behavior of glassy materials starting with simple Lennard Jones liquid. please advise me as to how to begin. a relevent flowchart or tutorial would be of immerse help thank you very much indeed. -- 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] request
hi do I need any .pdb file for making .gro and .top file? I make .pdb file with hyperchem software and then I used pdb2gmx command in order to make .gro and .top files. but I think my way is wrong. is it true? is there anybody that done this simulation? leila On Sun, Nov 21, 2010 at 11:24 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi, Define an itp file which has the non-bonded info. Then define a mdp (md parameter file) and also make a structure file (gro). Also you need a topology file (top) which corresponds to the structure file. You will have to do some background work. Manual should be your friend. amit On Sat, Nov 20, 2010 at 11:32 PM, leila separdar separdar.le...@gmail.com wrote: I am beginner with gromacs. I would like to simulate the behavior of glassy materials starting with simple Lennard Jones liquid. please advise me as to how to begin. a relevent flowchart or tutorial would be of immerse help thank you very much indeed. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] request
- Original Message - From: leila separdar separdar.le...@gmail.com Date: Sunday, November 21, 2010 19:15 Subject: Re: [gmx-users] request To: Discussion list for GROMACS users gmx-users@gromacs.org hi do I need any .pdb file for making .gro and .top file? I make .pdb file with hyperchem software and then I used pdb2gmx command in order to make .gro and .top files. but I think my way is wrong. is it true? Sounds OK. We don't have anywhere near enough information to tell. If you'd done some tutorial material and perhaps some simple normal GROMACS simulation of your own, you'd have more confidence in your capacity to design a workflow. Mark is there anybody that done this simulation? leila On Sun, Nov 21, 2010 at 11:24 AM, Amit Choubey kgp.a...@gmail.com wrote: Hi, Define an itp file which has the non-bonded info. Then define a mdp (md parameter file) and also make a structure file (gro). Also you need a topology file (top) which corresponds to the structure file. You will have to do some background work. Manual should be your friend. amit On Sat, Nov 20, 2010 at 11:32 PM, leila separdar separdar.le...@gmail.com wrote: I am beginner with gromacs. I would like to simulate the behavior of glassy materials starting with simple Lennard Jones liquid. please advise me as to how to begin. a relevent flowchart or tutorial would be of immerse help thank you very much indeed. -- gmx-users mailing list gmx-us...@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 list gmx-us...@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 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] question on KALP-15 in DPPC tutorial
Hi all, I was going through the very nicely presented tutorial by Justin (on KALP-15 in DPPC). I have one question regarding the non-bonded cut-offs. It seems that people use many different values of non-bonded cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i choose the cut-off values for my simulations ? amit -- 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] PR
Thank mark for comments, but I have check the structure after energy minimization through ramachandran plot and found 82% residues were lies in core region. After performed position restrained dynamics it reduced to 52% in core region also 1 bad contact was found. I have taken SPC water model then add 2 NA+ ions in the solvent, done energy minimization at emtol value of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position restraiuned dynamics, please let me know if any serious flaws. So help me by giving me the reference. title = Position restrained of Bcl-2. integrator = md define = -DPOSRES dt = 0.002 nsteps = 10 nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 xtc_grps = protein sol energygrps = protein sol ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.135 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Dispcorr = no Tcoupl = v-rescale tc-grps = protein sol NA+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds -- Pawan -- 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] extending simulation without cpt file
Hi, Today I use serach and find this topic. I got confused. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations According the page of extending simulation, in GROMACS ver.4, the commend is: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt I use this two lines to continue my simulation and get success. But now I'm much worried my data is wrong since I didn't use -e edr and -t trr as in the first line above. The way that tpbconv should -e -t files is written in the part ver. 3.3.3 and before. My GROMACS version is 4.0.5. Am I right to use lines above to do extending simulation? Hsin-Lin - Original Message - From: Yongchul Chung yxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-) 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] PR
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello, I haven't read the mails before, but as long as you are not in equilibrium I do not think that PR coupling is the best way to go. Furthermore PR is very sensitive to constraints and the time step, so perhaps 2fs is too large. Try to perform a simulations with the Berendsen thermostat to reach equilibrium and from there on turn on the PR coupling. Perhaps it is also a good idea to combine Parrinello-Rahman with the Nose-Hoover coupling scheme for the temperature as they are very similar. /Flo On 11/21/2010 11:09 AM, pawan raghav wrote: Thank mark for comments, but I have check the structure after energy minimization through ramachandran plot and found 82% residues were lies in core region. After performed position restrained dynamics it reduced to 52% in core region also 1 bad contact was found. I have taken SPC water model then add 2 NA+ ions in the solvent, done energy minimization at emtol value of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position restraiuned dynamics, please let me know if any serious flaws. So help me by giving me the reference. title = Position restrained of Bcl-2. integrator = md define = -DPOSRES dt = 0.002 nsteps = 10 nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 xtc_grps = protein sol energygrps = protein sol ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.135 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Dispcorr = no Tcoupl = v-rescale tc-grps = protein sol NA+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds -- Pawan - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzpDx4ACgkQLpNNBb9GiPm4pwCgnELG6jRU8HNptP9v7NzC++Uy 6SMAnRodoGiNjdvcnM4NQdyLmwt17w4y =VgDX -END PGP SIGNATURE- -- 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] find the relevant structure out
Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] question regarding to PMF calculation between 2 plates
Zhe, here's what comes to my mind. It certainly requires a whole bunch of testing, but if you really must calculate this then you could give it a try. In order to keep 2 plates planar, it seems to me that the distance between the planes must be controlled at 3 or more points (3 points defining a plane). Ideally, you can use 3 pull groups, each with a different reference group arranged in an equilateral triangle in one plane that each control the distance to a group in a similar triangle in the other plane. I would then do wham separately on each of the 3 pairs to get 3 evaluations of the PMF that I would average together. You could then redo this calculation for 4 points in a square, 5 points, etc. to quantify any systematic drift in the resulting answer as you increase the number of restraints and find the asymptote. I'm not sure if the newest pull code can handle multiple reference groups though. If not, then you might need to triangulate distances and do the pulling in XYZ with many more than 3 groups. Finally, if you want to get fancy and collate all of the data together from many pull groups prior to putting it into wham, then you'll need to rigorously ensure that you get the math right. I would personally use only one restrained distance set per wham calculation. Since I don't do anything like this myself, I can't add much more. Good luck. Chris. -- original message -- Dear GROMACS users, I have a question for calculating the potential of mean force between 2 plates (i.g., graphene) in water. It is not technically as simple as it seem. I found this question has been asked many times (I sum them up in the bottom of this note, so maybe it will be helpful for someone with similar question in future) but I cannot see a clear answer completely solving the problem. Information in the manual is quite limited on this topic as well. There are two ways I can see to do the calculation: 1. umbrella sampling; 2. free energy perturbation (JACS, 2005, 127, 3556). Both of them, however, need to deal with 2 questions first in order to get any meaningful result: 1. keep the plates to be really plates (flat surface); 2. inhibit plate rotation. There are 3 ways that come into my mind to solve these 2 problems, but none of them works as I tried. (Similar idea has been suggested in the previous posts regarding to the problem.) I am using a simple NPT system in the free energy perturbation scheme, because it is physically more meaningful and simpler to test than umbrella potential. But problem comes from the 3 method I tried: 1) Merely constructing a really complicated itp file with bond, angle, dihedral, imp dihedral cannot easily maintain a planar plate. Rotation of the plates is not easy to deal with, which I still don't have any idea yet. (Someone suggested other methods rather than this one in the previous post.) 2) Freezing all plates will make the plates do what they should do, but there is problem with the pressure coupling according to the manual. GMX 4.0.x wouldn't work as specified in the manual. GMX 3.3.3 works as it seems but the system is very easy to blow up. 3) Use position RESTRAINT on all atoms on the plates in XYZ direction (basically fixing them in the initial position) as suggested in previous posts. As an example: --- [ position_restraints ] ; ai funct fc 1 195000 95000 95000 2 195000 95000 95000 3 195000 95000 95000 4 195000 95000 95000 every atom in the plates However, or small force constant, the plate won't be maintained. For large force constant (the above example), the system will easily blow up even with time step of 1fs. For sure, once we have too large vibration in the system, an even smaller time step is required. Then the efficiency is going to be really really low. (To provide further details: I minimize the system with both steep and cg first and run the 400 ps NVT(Nose) run before the NPT (Parrinello, isotropic or semiisotropic) run. The test system is fairly small: 570 waters (SPC/E) with 2 plates of graphene (60 atoms each, amber parameters). So there should not be problem with the equilibration. I tuned the force constant in the restraint to see whether the plate change or not.) I will really appreciate it if someone can suggest some way out or where my problem is in the simulation. Is it the right way of restraining the system? Is there better way of doing this? It will be great if discussions coming along. Thank you in advanced for your help! (There has been tons of paper doing this with some other package, I am sure GROMACS can do it. I am just not the person who can figure this out.) Thanks, Zhe Links for the previous representative post related:
Re: [gmx-users] find the relevant structure out
On 21/11/2010 11:43 PM, #ZHAO LINA# wrote: Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-) 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] PR
On 21/11/2010 9:09 PM, pawan raghav wrote: Thank mark for comments, but I have check the structure after energy minimization through ramachandran plot and found 82% residues were lies in core region. After performed position restrained dynamics it reduced to 52% in core region also 1 bad contact was found. I have taken SPC water model then add 2 NA+ ions in the solvent, done energy minimization at emtol value of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position restraiuned dynamics, please let me know if any serious flaws. So help me by giving me the reference. title = Position restrained of Bcl-2. integrator = md define = -DPOSRES dt = 0.002 A smaller timestep during equilibration will better help the integration cope with anything that is not very happy. nsteps = 10 nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 xtc_grps = protein sol energygrps = protein sol ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.135 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Dispcorr = no Tcoupl = v-rescale tc-grps = protein sol NA+ Those groups are bad. See http://www.gromacs.org/Documentation/Terminology/Thermostats Mark tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds -- Pawan -- 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] extending simulation without cpt file
On 21/11/2010 10:58 PM, Hsin-Lin Chiang wrote: Hi, Today I use serach and find this topic. I got confused. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations According the page of extending simulation, in GROMACS ver.4, the commend is: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr So you've created a new .tpr with a longer simulation time (but which incidentally has the state of the previous .tpr)... mdrun -s next.tpr -cpi previous.cpt ... and told mdrun to use that longer time, and the current state in the checkpoint file. This will work, so long as you are not attempting to change the thermodynamic ensemble, or similar. Mark I use this two lines to continue my simulation and get success. But now I'm much worried my data is wrong since I didn't use -e edr and -t trr as in the first line above. The way that tpbconv should -e -t files is written in the part ver. 3.3.3 and before. My GROMACS version is 4.0.5. Am I right to use lines above to do extending simulation? Hsin-Lin - Original Message - From: Yongchul Chung yxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS users gmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-) 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] xtc corrupted during REMD
On 21/11/2010 2:34 AM, Spitaleri Andrea wrote: Hi there, I am encountering a weird problem with a REMD simulation using 4.5.3. The total simulation is 50ns with 5 replica, and I do in two runs: 25ns and then continuing to 50ns (walltime queue). The first run is okay, the continue run (the last 25ns) randomly make some xtc files corrupted (from gmxcheck I get the Magic Number Error). I don't understand how the simulation can continue writing the .xtc files when you are getting magic number errors from gmxcheck. We need to see command lines for your workflow, please :-) Mark It is strange since the respective trr files are okay and the simulation is still going (it is not blowing up from the log, not step.pdb files, not crash). The only difference is that I am writing the xtc often respect to the trr file and just the complex not the solvent: nstxout = 1 ; coordinates every 20ps nstvout = 0 ; velocity every 0ps nstfout = 0 ; forces every 0 ps nstlog = 2500 ; energies log every 5ps nstenergy = 2500 ; energies every 5ps nstxtcout = 2500 ; coordinates every 5ps to xtc xtc-precision = 2500 ; xtc-grps= complex; Since the error is happening only for the continuing run, I am just wondering if there is any reason for this. thanks for any help and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- 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] question on KALP-15 in DPPC tutorial
On 21/11/2010 8:45 PM, Amit Choubey wrote: Hi all, I was going through the very nicely presented tutorial by Justin (on KALP-15 in DPPC). I have one question regarding the non-bonded cut-offs. It seems that people use many different values of non-bonded cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i choose the cut-off values for my simulations ? In the first instance, by reproducing the conditions under which the parameters were validated. Unfortunately, most of the force fields were not parametrized for PME, under which they are often now used. So look at some papers from large well-known groups that have done something similar to what you want to do, judge how well they have worked, and do something comparable. Unfortunately, there have been little or no systematic studies of how accurate forcefield X plus PME needs to be to model reality usefully. Hopefully that will change :-) 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] question on KALP-15 in DPPC tutorial
Quoting Mark Abraham mark.abra...@anu.edu.au: On 21/11/2010 8:45 PM, Amit Choubey wrote: Hi all, I was going through the very nicely presented tutorial by Justin (on KALP-15 in DPPC). I have one question regarding the non-bonded cut-offs. It seems that people use many different values of non-bonded cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i choose the cut-off values for my simulations ? In the first instance, by reproducing the conditions under which the parameters were validated. Unfortunately, most of the force fields were not parametrized for PME, under which they are often now used. So look at some papers from large well-known groups that have done something similar to what you want to do, judge how well they have worked, and do something comparable. Unfortunately, there have been little or no systematic studies of how accurate forcefield X plus PME needs to be to model reality usefully. Hopefully that will change :-) And directly related to the tutorial in question, the settings used therein were assigned to reproduce the study that I cite in the introductory material. -Justin Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
R: [gmx-users] xtc corrupted during REMD
Hi, yes sure. Basically I do: 1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 - i get the first 5x25ns of remd simulation (five xtc every 5ps and five trr every 20ps, for each replica). I check those files by gmxcheck and they are fine. no errors. 2. for i in 'seq 1 5'; tpbconv -s runA_$i -nsteps 2500 -o runB_$i - extension the simulation to 50ns total 3. mdrun -s runB_ -replex 5000 -multi 5 -deffnm runB_ -cpi runA_ - at end some (2 or 1 on the 5 xtc file) of the xtc are corrupted (from gmxcheck) whereas the trr are fine. These are from 25ns to 50ns. From the log file I do not see any errors. Everything seems fine. I have free room space in the hd too :) I am just wondering whether the problem is in the xtc options (precision and writing step) thanks a lot and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di Mark Abraham [mark.abra...@anu.edu.au] Inviato: domenica 21 novembre 2010 17.03 A: Discussion list for GROMACS users Oggetto: Re: [gmx-users] xtc corrupted during REMD On 21/11/2010 2:34 AM, Spitaleri Andrea wrote: Hi there, I am encountering a weird problem with a REMD simulation using 4.5.3. The total simulation is 50ns with 5 replica, and I do in two runs: 25ns and then continuing to 50ns (walltime queue). The first run is okay, the continue run (the last 25ns) randomly make some xtc files corrupted (from gmxcheck I get the Magic Number Error). I don't understand how the simulation can continue writing the .xtc files when you are getting magic number errors from gmxcheck. We need to see command lines for your workflow, please :-) Mark It is strange since the respective trr files are okay and the simulation is still going (it is not blowing up from the log, not step.pdb files, not crash). The only difference is that I am writing the xtc often respect to the trr file and just the complex not the solvent: nstxout = 1 ; coordinates every 20ps nstvout = 0 ; velocity every 0ps nstfout = 0 ; forces every 0 ps nstlog = 2500 ; energies log every 5ps nstenergy = 2500 ; energies every 5ps nstxtcout = 2500 ; coordinates every 5ps to xtc xtc-precision = 2500 ; xtc-grps= complex; Since the error is happening only for the continuing run, I am just wondering if there is any reason for this. thanks for any help and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- 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 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- 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] question on KALP-15 in DPPC tutorial
Thank you Mark and Justin. Yes i did check the reference of your tutorial, but its just that there are so many groups using same FF but different cut-off lengths. amit On Sun, Nov 21, 2010 at 10:22 AM, Justin A. Lemkul jalem...@vt.edu wrote: Quoting Mark Abraham mark.abra...@anu.edu.au: On 21/11/2010 8:45 PM, Amit Choubey wrote: Hi all, I was going through the very nicely presented tutorial by Justin (on KALP-15 in DPPC). I have one question regarding the non-bonded cut-offs. It seems that people use many different values of non-bonded cut-off (varying from 0.9 nm to 1.2 nm or probably more). How should i choose the cut-off values for my simulations ? In the first instance, by reproducing the conditions under which the parameters were validated. Unfortunately, most of the force fields were not parametrized for PME, under which they are often now used. So look at some papers from large well-known groups that have done something similar to what you want to do, judge how well they have worked, and do something comparable. Unfortunately, there have been little or no systematic studies of how accurate forcefield X plus PME needs to be to model reality usefully. Hopefully that will change :-) And directly related to the tutorial in question, the settings used therein were assigned to reproduce the study that I cite in the introductory material. -Justin Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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] find the relevant structure out
do_dssp -f traj.xtc -s topol.tpr -o ss.xpm trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump Took several frames, here, such as model 1000, model 3000 and model 5000, and named as 1000.pbd, 3000.pdb and 5000.pdb pymol 3000.pdb intra_fit protein and (name c,n,ca) show cartoon all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. what are those files I should have looked for, and how could I find a better way to show those beta-sheet out? Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Sunday, November 21, 2010 11:58 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] find the relevant structure out On 21/11/2010 11:43 PM, #ZHAO LINA# wrote: Hi, I had done 10ns simulation, by dssp, can see the beta-sheet appeared very apparently, before it's alpha-helix. there were 5000 frames, I based on the time of the picture got from dssp, I can guess around which frames is supposed to have those beta sheets. After I took few frames which I thought might be representive, but under pymol, show cartoon, there is none beta sheet at all. There were 5000 frames, I really do not know which one is most representive. Or maybe some parts I understand wrong. Thanks for any advice and if I am wrong please let me know, We've really no idea of the detail of what you've done, so can't guess. Just about anything could be the problem - all the way from you are looking at the wrong files, to pymol's definition of a beta sheet doesn't agree with dssp. If you can't report the command lines you used easily, then your method was not reproducible enough, or not recorded well enough :-) 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] extending simulation without cpt file
Hi, Mark So, You mean I can get correct extending simulation without using -e ede and -t trr in GROMACS ver.4. Then I can set my mind at rest. Thank you for your reply. Hsin-Lin Hi, Today I use serach and find this topic. I got confused. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations According the page of extending simulation, in GROMACS ver.4, the commend is: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr So you've created a new .tpr with a longer simulation time (but which incidentally has the state of the previous .tpr)... mdrun -s next.tpr -cpi previous.cpt ... and told mdrun to use that longer time, and the current state in the checkpoint file. This will work, so long as you are not attempting to change the thermodynamic ensemble, or similar. Mark I use this two lines to continue my simulation and get success. But now I'm much worried my data is wrong since I didn't use -e edr and -t trr as in the first line above. The way that tpbconv should -e -t files is written in the part ver. 3.3.3 and before. My GROMACS version is 4.0.5. Am I right to use lines above to do extending simulation? Hsin-Lin - Original Message - From: Yongchul Chungyxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS usersgmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How-tos/Extending_Simulations). I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulation starts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-) Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20101122/437e2152/attachment.html -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] question regarding to PMF calculation between 2 plates
Hi Chris, Thank you so much for the idea! It is a good idea of using umbrella sampling technique. But I am not sure whether it is just a matter of averaging 3 PMFs as the final result. To be physical, we need the 2 plates to be parallel to each other at any time, right? With 3 pull groups (or more groups), indeed we defined 2 plates. But in simulation, independent variation of these 3 distances will make angles between the plates. The angles could be large when the umbrella is relatively small, as a balance between distribution overlap and # of windows. For sure, their average behavior should be parallel, but I don't know whether simple averaged PMFs is physical. Of course, trying 4 or 5 pull groups as tests will be helpful to examine this idea. Meanwhile, we still need to deal with the rigidity of the plates: to make sure they are flat during the simulation. So as I can see, it is inevitable to use some sort restraint in the system anyway. That is a reason why I used position restraint (PR) as mentioned in my last email. As long as PR works in the NPT, I can just simply use the potential obtained, followed by free energy perturbation scheme, get the PMF. The problem is, the PR doesn't work in NPT in my test cases. Again, thank you very much for helping me with your idea! I really appreciate it. I am now testing even smaller time steps to see whether PR will work (as suggested in discussion from Pawan, Florian and Mark in a few emails after my post). Will keep you updated for any new progress. Sure, further ideas will be really appreciated. Thanks, Zhe On Sun, Nov 21, 2010 at 9:46 AM, chris.ne...@utoronto.ca wrote: Zhe, here's what comes to my mind. It certainly requires a whole bunch of testing, but if you really must calculate this then you could give it a try. In order to keep 2 plates planar, it seems to me that the distance between the planes must be controlled at 3 or more points (3 points defining a plane). Ideally, you can use 3 pull groups, each with a different reference group arranged in an equilateral triangle in one plane that each control the distance to a group in a similar triangle in the other plane. I would then do wham separately on each of the 3 pairs to get 3 evaluations of the PMF that I would average together. You could then redo this calculation for 4 points in a square, 5 points, etc. to quantify any systematic drift in the resulting answer as you increase the number of restraints and find the asymptote. I'm not sure if the newest pull code can handle multiple reference groups though. If not, then you might need to triangulate distances and do the pulling in XYZ with many more than 3 groups. Finally, if you want to get fancy and collate all of the data together from many pull groups prior to putting it into wham, then you'll need to rigorously ensure that you get the math right. I would personally use only one restrained distance set per wham calculation. Since I don't do anything like this myself, I can't add much more. Good luck. Chris. -- original message -- Dear GROMACS users, I have a question for calculating the potential of mean force between 2 plates (i.g., graphene) in water. It is not technically as simple as it seem. I found this question has been asked many times (I sum them up in the bottom of this note, so maybe it will be helpful for someone with similar question in future) but I cannot see a clear answer completely solving the problem. Information in the manual is quite limited on this topic as well. There are two ways I can see to do the calculation: 1. umbrella sampling; 2. free energy perturbation (JACS, 2005, 127, 3556). Both of them, however, need to deal with 2 questions first in order to get any meaningful result: 1. keep the plates to be really plates (flat surface); 2. inhibit plate rotation. There are 3 ways that come into my mind to solve these 2 problems, but none of them works as I tried. (Similar idea has been suggested in the previous posts regarding to the problem.) I am using a simple NPT system in the free energy perturbation scheme, because it is physically more meaningful and simpler to test than umbrella potential. But problem comes from the 3 method I tried: 1) Merely constructing a really complicated itp file with bond, angle, dihedral, imp dihedral cannot easily maintain a planar plate. Rotation of the plates is not easy to deal with, which I still don't have any idea yet. (Someone suggested other methods rather than this one in the previous post.) 2) Freezing all plates will make the plates do what they should do, but there is problem with the pressure coupling according to the manual. GMX 4.0.x wouldn't work as specified in the manual. GMX 3.3.3 works as it seems but the system is very easy to blow up. 3) Use position RESTRAINT on all atoms on the plates in XYZ direction (basically fixing them in the initial position) as suggested in previous posts. As an example:
Re: [gmx-users] extending simulation without cpt file
- Original Message - From: Hsin-Lin Chiang jian...@phys.sinica.edu.tw Date: Monday, November 22, 2010 14:51 Subject: Re: [gmx-users] extending simulation without cpt file To: gmx-users@gromacs.org Hi, Mark So, You mean I can get correct extending simulation without using -e ede and -t trr in GROMACS ver.4. Yes. That's what the link you gave says. Mark Then I can set my mind at rest. Thank you for your reply. Hsin-Lin Hi, Today I use serach and find this topic. I got confused. http://www.gromacs.org/Documentation/How-tos/Extending_Simulations According the page of extending simulation, in GROMACS ver.4, the commend is: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr So you've created a new .tpr with a longer simulation time (but which incidentally has the state of the previous .tpr)... mdrun -s next.tpr -cpi previous.cpt ... and told mdrun to use that longer time, and the current state in the checkpoint file. This will work, so long as you are not attempting to change the thermodynamic ensemble, or similar. Mark I use this two lines to continue my simulation and get success. But now I'm much worried my data is wrong since I didn't use - e edr and -t trr as in the first line above. The way that tpbconv should -e -t files is written in the part ver. 3.3.3 and before. My GROMACS version is 4.0.5. Am I right to use lines above to do extending simulation? Hsin-Lin - Original Message - From: Yongchul Chungyxc...@case.edu Date: Thursday, November 4, 2010 10:28 Subject: [gmx-users] extending simulation without cpt file To: Discussion list for GROMACS usersgmx-users@gromacs.org Hello gmxers, I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but erased cpt file. However, I need to extend the simulation from the end of the trajectory file. I know this will not be binary identical as stated here (http://www.gromacs.org/Documentation/How- tos/Extending_Simulations).I used following commands. tpbconv -s topol.tpr -extend 102000 -o topolnew.tpr mdrun -s topolnew.tpr When I do this and run the simulation, for some reason, the simulationstarts from t=0 instead of t=102000. it seems like gromacs is writing the file without recognizing it that it should start the trajectory from 102000 ps. Is this a known bug? If so, is there a way around to solve this problem? You've extended the run time of the original simulation, and forced it to start from the state in the new .tpr, but that state came from the original .tpr. By contrast, mdrun -s -cpi replaces the .tpr state with that of the checkpoint. Your best chance of continuing will come from reconstructing the .mdp suitably (use gmxcheck to compare resulting .tpr files) and using grompp to create a .tpr using the most recent endpoint permitted by your .trr + .edr. Actually, Justin's right. tpbconv needs -e -t files. It's been so long since I used it, I'd forgotten :-) Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx- users/attachments/20101122/437e2152/attachment.html -- -- 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] PR
Thank you for the discussion. I am basically having a similar problem: position restraining (PR) 2 plates in NPT and the system blow up (posted here: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055975.html). I will try to use smaller time step to see whether the situation becomes better. A quick question, can we really do meaningful NPT simulation with PR, in which the position need to be almost like fixed? I know we cannot do freeze. PR supposed to be OK, right? Thanks, Zhe On Sun, Nov 21, 2010 at 9:51 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 21/11/2010 9:09 PM, pawan raghav wrote: Thank mark for comments, but I have check the structure after energy minimization through ramachandran plot and found 82% residues were lies in core region. After performed position restrained dynamics it reduced to 52% in core region also 1 bad contact was found. I have taken SPC water model then add 2 NA+ ions in the solvent, done energy minimization at emtol value of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position restraiuned dynamics, please let me know if any serious flaws. So help me by giving me the reference. title = Position restrained of Bcl-2. integrator = md define = -DPOSRES dt = 0.002 A smaller timestep during equilibration will better help the integration cope with anything that is not very happy. nsteps = 10 nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 xtc_grps = protein sol energygrps = protein sol ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.135 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Dispcorr = no Tcoupl = v-rescale tc-grps = protein sol NA+ Those groups are bad. See http://www.gromacs.org/Documentation/Terminology/Thermostats Mark tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.0 gen_seed = 173529 constraints = all-bonds -- Pawan -- gmx-users mailing list gmx-us...@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] xtc corrupted during REMD
On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea spitaleri.and...@hsr.itwrote: Hi, yes sure. Basically I do: 1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 - i get the first 5x25ns of remd simulation (five xtc every 5ps and five trr every 20ps, for each replica). I check those files by gmxcheck and they are fine. no errors. 2. for i in 'seq 1 5'; tpbconv -s runA_$i -nsteps 2500 -o runB_$i - extension the simulation to 50ns total 3. mdrun -s runB_ -replex 5000 -multi 5 -deffnm runB_ -cpi runA_ - at end some (2 or 1 on the 5 xtc file) of the xtc are corrupted (from gmxcheck) whereas the trr are fine. These are from 25ns to 50ns. From the log file I do not see any errors. Everything seems fine. I have free room space in the hd too :) I am just wondering whether the problem is in the xtc options (precision and writing step) I doubt it that it has anything to do with your xtc options. Are all you xtc corrupted or only some? Are those which are corrupted all corrupted on the same frame or different ones? Roland Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di Mark Abraham [mark.abra...@anu.edu.au] Inviato: domenica 21 novembre 2010 17.03 A: Discussion list for GROMACS users Oggetto: Re: [gmx-users] xtc corrupted during REMD On 21/11/2010 2:34 AM, Spitaleri Andrea wrote: Hi there, I am encountering a weird problem with a REMD simulation using 4.5.3. The total simulation is 50ns with 5 replica, and I do in two runs: 25ns and then continuing to 50ns (walltime queue). The first run is okay, the continue run (the last 25ns) randomly make some xtc files corrupted (from gmxcheck I get the Magic Number Error). I don't understand how the simulation can continue writing the .xtc files when you are getting magic number errors from gmxcheck. We need to see command lines for your workflow, please :-) Mark It is strange since the respective trr files are okay and the simulation is still going (it is not blowing up from the log, not step.pdb files, not crash). The only difference is that I am writing the xtc often respect to the trr file and just the complex not the solvent: nstxout = 1 ; coordinates every 20ps nstvout = 0 ; velocity every 0ps nstfout = 0 ; forces every 0 ps nstlog = 2500 ; energies log every 5ps nstenergy = 2500 ; energies every 5ps nstxtcout = 2500 ; coordinates every 5ps to xtc xtc-precision = 2500 ; xtc-grps= complex; Since the error is happening only for the continuing run, I am just wondering if there is any reason for this. thanks for any help and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- 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 --- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org -- 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
Re: [gmx-users] Pairwise forces
Thanks a lot for the replies. What we would like to have are the pairwise forces. I, however, was not sure if gromacs saves the pairwise forces to the trajectory file or not (I now figured out with gmxdump that atomic forces are saved). I also came across the mdrun -rerun option, but I was not entirely sure if it would save me time. I will give it a try with FDA gromacs. Kind regards, Reiner Am 20.11.2010 15:47, schrieb Bogdan Costescu: On Fri, Nov 19, 2010 at 12:15, Reiner Ribarics reiner.ribar...@meduniwien.ac.at wrote: Our group has already done some rather long simulations and according to the script files forces are written every 1 steps and can be accessed via trjconv with -cf option that assigns each atom a temperature factor. I was wondering if that is the way gromacs stores the forces in the trajectory file. Or are the temperature factors calculated from other (maybe pairwise) forces? It's not clear to me what you try to do. Obtain atomic forces ? Obtain pairwise forces ? Know the format in which forces are stored in the trajectory file ? Something else entirely ? I also had a look at FDA gromacs that is able to write out pairwise forces, but unfortunately it falls back on the rather slow gromacs routines and we want to avoid rerunning our simulations if possible. Then please take a look again. The forces are indeed saved by hooking into the C kernels, but in a 'mdrun -rerun' phase which reads back the trajectory and writes the forces, which avoids having a compute intensive phase with the C kernels and the FDA modifications. Kind regards, Bogdan -- Mag. Reiner Ribarics Unit for Medical Statistics and Informatics Section for Biomedical Computersimulation and Bioinformatics Medical University of Vienna General Hospital Spitalgasse 23, BT88 A-1090 Vienna http://www.meduniwien.ac.at/msi/biosim/ -- 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] potassium ion incorporation in GROMOS53a6 forcefield
Dear all, Can anybody tell me how to incorporate potassium ion parameters in GROMACS for GROMOS53a6 forcefield. Thanking you in anticipation. With regards, Jignesh -- 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
