Re: [gmx-users] g_msd and diffusion coefficent
- Original Message - From: leila karami Date: Tuesday, June 29, 2010 16:41 Subject: [gmx-users] g_msd and diffusion coefficent To: gmx-users@gromacs.org > Hi gromacs users > > in my system, there are pr, dna, water and Na and I > want to obtain diffusion of pr in dna but when I use g_msd command, gromacs > says select only 1 group. should be this group pr or dna? What's pr? If you mean protein, does it make sense to find the diffusion coefficient of a protein within DNA? What does it make sense to find a diffusion coefficient in? 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_msd and diffusion coefficent
Dear Mark Abraham yes. pr means protein. I want to obtain diffusion of protein within dna. I want to know how/how much pr diffuse to dna. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_msd and diffusion coefficent
- Original Message - From: leila karami Date: Tuesday, June 29, 2010 17:32 Subject: [gmx-users] g_msd and diffusion coefficent To: gmx-users@gromacs.org > Dear Mark Abraham > > yes. pr means protein. I want to obtain diffusion of > protein within dna. I want to know how/how much pr diffuse to dna. No, you probably don't. "within" and "to" mean different things. You probably want to measure something about the diffusion of your protein in water (the solvent!) in the presence of DNA. If you're trying to deduce something about the frequency of protein-DNA binding events, then you'll probably need a ridiculously long and large simulation with lots of such events in order to deduce anything comparable with any experimental data. 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_msd and diffusion coefficent
Dear Mark Abraham No, I want to measure something about the diffusion of my protein to DNA (especially to major groove of DNA) in the presence of water (as solvent). -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Technical
Dear Justin, Thanks for the wonderful suggestions which is very clear and informative but I am confused about some points below 1. Actually my protein is human mitochondrial protein so I have used GROMOS 96 53a6 ff. is it correct? but you have mentioned about the condition applied, so I don't understand this point because I have a normal protein which bind on the mitochondrial membrane. So according to you which conditions should i applied? which preferences you are talking about? Due to have limited configuration of our hardware we are using core2duo single processor with 4 GB RAM. So dear please suggest me the concise requirements for this simulation. 2. My protein does not depend on the temperature that means it is not thermophilic or mesophilic protein. So for large simulations is it correct to apply REMD technique. I think that ED sampling should be best but don't know which should be taken for reference structure. I have tell you about my system and protein so please suggest me the sampling technique is effective in my protein case. 3. I know about the energy conservation but don't know about the simulation stability. So please also tell me is PCA should be performed for simulation stability or something else analysis should be performed. 4. Why 4-5 fs is more effecient than 3fs? -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: g_msd and diffusion coefficent
Use NDX file. Dr. Vitaly V. Chaban > > in my system, there are pr, dna, water and Na and I want to obtain diffusion > of pr in dna but when I use g_msd command, gromacs says select only 1 > group. should be this group pr or dna? > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] liquid-vapor
Hi, Is there a standard trick in gromacs to get the atom numbers which are located in the liquid-vapor interface? Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_msd and diffusion coefficent
Dear Vitaly Chaban I know using index file but gromacs say : select only 1 group. what is this group ? protein? or DNA? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_msd and diffusion coefficent
- Original Message - From: leila karami Date: Tuesday, June 29, 2010 18:08 Subject: [gmx-users] g_msd and diffusion coefficent To: gmx-users@gromacs.org > Dear Mark Abraham> No, I want to measure something about the diffusion of my > protein to DNA (especially to major groove of DNA) in the presence of water > (as solvent). Well if you have a trajectory that diffuses the protein to your DNA, then measure the diffusion coefficient by choosing the protein group in g_rmsd. The analysis program doesn't need to know why you chose that trajectory. Finding a meaningful set of such a trajectories can be tough, however. 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error while loading shared libraries: libOpenMM.so:
Hi, You also need the OpenMM libraries and plugins. For more detail see: http://www.gromacs.org/gpu#Installing_and_running_Gromacs-GPU -- Szilárd On Sat, Jun 26, 2010 at 6:18 PM, Tarsis wrote: > I'm trying to install cuda but when I export > LD_LIBRARY_PATH=/usr/local/cuda/lib:$libcudart.so I get a message: > > ./gromacs-4.0.7/bin/mdrun-gpu: error while loading shared libraries: > libOpenMM.so: cannot open shared object file: No such file or directory > > after running mdrun -h > > thanks in advance > > Tarsis > -- > Tarsis Gesteira Ferreira, MSc. > UNIFESP, Department of Biochemistry. > Rua Três de Maio, nº 100, quarto andar. > CEP 04044-020; São Paulo, Brasil. > Office: +551155764442 r220 > Cel: +551176570135 > > > -- > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] b-factor
Hi all pdb file for my protein was obtained by solution NMR. this file is as follows : ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00 ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00 ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00 ATOM 4 O GLY A 1 -23.652 -6.939 2.393 1.00 0.00 ATOM 5 H1 GLY A 1 -26.109 -7.957 4.035 1.00 0.00 ATOM 6 HA2 GLY A 1 -24.067 -7.811 5.488 1.00 0.00 ATOM 7 HA3 GLY A 1 -23.324 -8.902 4.328 1.00 0.00 ATOM 8 N SER A 2 -23.111 -5.869 4.298 1.00 0.00 pdb file obtaind from g_rmsf -f pr.xtc -s pr.tpr -n pr.ndx -oq command is as follws : ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00 272.65 ATOM 12 CA SER 2 23.444 51.157 35.390 1.00 257.41 ATOM 23 CA SER 3 25.254 48.487 33.290 1.00 189.09 ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00 114.27 ATOM 41 CA SER 5 27.814 48.657 27.860 1.00 195.51 ATOM 52 CA SER 6 31.164 48.167 26.020 1.00 217.99 ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00 300.70 ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00 248.64 so can I compare experimental B-factor with that calculated from MD? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:g_msd and diffusion coefficent
> Message: 5 > Date: Tue, 29 Jun 2010 11:54:12 +0330 > From: leila karami > Subject: [gmx-users] g_msd and diffusion coefficent > To: gmx-users@gromacs.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Vitaly Chaban > > I know using index file but gromacs say : select only 1 group. what is this > group ? protein? or DNA? It is not clear what exactly you want. To observe as one molecule moves in relation to another one? If this would have been my task, I would introduce some specific function of the distance between them vs time. Is it not easier just to calculate two diffusion constants corresponding to your particles of interest? Is it equilibrium MD that you perform? Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gromacs with CMAP
HI, David, thanks for your advise. I remove the bond angle force and get same result. It is really strange. If I set +5 on all the 24*24 grid, I just get a inverted distribution and if I set 0 on all grid, I will get a uniformed distribution. It is like that 27 regions are force to have zero cmap potential. I cannot attach figure due to size limit the list. I have sent the figure to you directly. best, dawei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gromacs with CMAP
Hi, I do not fully understand what you are trying to do, but currently CMAP is only available for the standard amino acid residues present in the rtp-file for the Charmm-forcefield, and the values for the grid are specified in the cmap.itp-file. Do you use something else? /Per 29 jun 2010 kl. 14.45 skrev Da-Wei Li: > HI, David, > > thanks for your advise. I remove the bond angle force and get same > result. It is really strange. If I set +5 on all the 24*24 grid, I > just get a inverted distribution and if I set 0 on all grid, I will > get a uniformed distribution. It is like that 27 regions are force to > have zero cmap potential. I cannot attach figure due to size limit the > list. I have sent the figure to you directly. > > best, > > dawei > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gromacs with CMAP
It is because I want to apply cmap to my own stuff. I can define my own 2D grid potential and apply to two sequential dihedral angles by add one line in the topol file. However, the testing result is really unexpected. dawei On Tue, Jun 29, 2010 at 8:53 AM, Per Larsson wrote: > Hi, > > I do not fully understand what you are trying to do, but currently CMAP is > only > available for the standard amino acid residues present in the rtp-file for the > Charmm-forcefield, and the values for the grid are specified in the > cmap.itp-file. > > Do you use something else? > > /Per > > > 29 jun 2010 kl. 14.45 skrev Da-Wei Li: > >> HI, David, >> >> thanks for your advise. I remove the bond angle force and get same >> result. It is really strange. If I set +5 on all the 24*24 grid, I >> just get a inverted distribution and if I set 0 on all grid, I will >> get a uniformed distribution. It is like that 27 regions are force to >> have zero cmap potential. I cannot attach figure due to size limit the >> list. I have sent the figure to you directly. >> >> best, >> >> dawei >> -- >> 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/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] multiple time step
Dear All, Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. Kind regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] different ref_t
I try to simulate a small peptide in CHCl3 there the peptide is couplet to a heat bath at a different temperature: tcoupl = nose-hoover tc-grps = Protein+PTS+AIC CHCl3 tau_t = 0.01 0.01 ref_t = 220 300 If I do so the temperature of the CHCl3 molecules drop down to almost 0K and the temperature of the peptide increases significantly. Has someone any experience with such a system and can give me a hint what to do? Thanks a lot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Technical
pawan raghav wrote: Dear Justin, Thanks for the wonderful suggestions which is very clear and informative but I am confused about some points below 1. Actually my protein is human mitochondrial protein so I have used GROMOS 96 53a6 ff. is it correct? but you have mentioned about the There is no immediate connection in my mind between a mitochondrial protein and GROMOS96 53A6. How did you jump to this conclusion? condition applied, so I don't understand this point because I have a normal protein which bind on the mitochondrial membrane. So according to Now here is a major consideration. Are you modeling the membrane as well, or just the protein? If you are modeling the membrane, the choice of force field becomes more complicated. There are numerous lipid parameter sets - Berger and Kukol united-atom sets, OPLS-AA and CHARMM all-atom sets. you which conditions should i applied? which preferences you are talking about? Due to have limited configuration of our hardware we are using core2duo single processor with 4 GB RAM. So dear please suggest me the concise requirements for this simulation. No. You have to do your own homework. The most challenging part of any simulation is planning it. You have to do the legwork of reading about the protein force fields, and maybe the lipid force fields as well (which you haven't mentioned). 2. My protein does not depend on the temperature that means it is not thermophilic or mesophilic protein. So for large simulations is it correct to apply REMD technique. I think that ED sampling should be best but don't know which should be taken for reference structure. I have tell you about my system and protein so please suggest me the sampling technique is effective in my protein case. The type of method you employ is based on what you want to observe. You said you wanted to sample loop dynamics, for which you can either run several simulations at the relevant (physiological?) temperature and analyze those results to obtain some averages, or you can apply REMD. I don't know how useful ED/PCA would be here, but it is a post-processing analysis technique, so it won't help you in sampling. 3. I know about the energy conservation but don't know about the simulation stability. So please also tell me is PCA should be performed for simulation stability or something else analysis should be performed. These two concepts are unrelated. Stability simply means the model physics doesn't break down and your simulation actually runs. 4. Why 4-5 fs is more effecient than 3fs? I mentioned this for several reasons. First, you collect more data faster. But if you're using lipids (note how this is a major consideration!) then preparing these topologies is not trivial. You basically have to write the topology by hand. Processing a protein with virtual sites is easy with pdb2gmx. Second, I have a minor pet peeve when I see a 3 fs timestep in the literature along with a claim like "simulations were conducted for 100 ns using a 3 fs timestep." That's mathematically impossible, so I think the reporting is inaccurate. But that's just me :) And besides, if you're going to extend the timestep, why not go all the way and really utilize the performance GROMACS offers? -Justin -- Pawan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rdf has a huge memory leak.
Hi everyone: I am using g_rdf to calculate radial distribution function. However when I check the memory usage using top, it seems to me that the code has a huge memory leak. My system has 4GB memory but it usually has 40MB free memory left after the program finishes. Does anyone have the same problem before? Thanks, Kun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_rdf has a huge memory leak.
Hi Kun, Can you tell more about what you are doing? What are you analyzing? How large is the system? Which groups do you use for analysis. Etc., etc. Now, you might be right, but you might as well be jumping to conclusions. Cheers, Tsjerk On Tue, Jun 29, 2010 at 4:12 PM, Kun Huang wrote: > Hi everyone: > > I am using g_rdf to calculate radial distribution function. However when I > check the memory usage using top, it seems to me that the code has a huge > memory leak. My system has 4GB memory but it usually has 40MB free memory > left after the program finishes. > > Does anyone have the same problem before? > > Thanks, > Kun > > -- > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] multiple time step
multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this. -- original message -- Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. Kind regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] different ref_t
Can you please supply gen_temp and also your pressure coupling values? Also, please supply the g_energy values that show the temperatures changing as you suggest (with accompanying timestep info). I'm fairly sure that what is happening is that you are simply seeing the nose-hoover oscillations (possibly coupled to your pressure coupling fluctuations) and since your CHCl3 is presumably very small then you see a larger effect on it. I'd suggest doing a few tests: 1. Increase tau_t to 0.1 or perhaps 0.4 (I don't use nose-hoover, but your value seems small). 2. Run longer and see if it is indeed a fluctuation and not just a trend to zero. 3. Why not try the SD integrator? And a PS that I'm simply assuming that you know what you're doing with 2 different temperatures since you didn't ask for advice on that part. Chris. -- original message -- I try to simulate a small peptide in CHCl3 there the peptide is couplet to a heat bath at a different temperature: tcoupl = nose-hoover tc-grps = Protein+PTS+AIC CHCl3 tau_t = 0.01 0.01 ref_t = 220 300 If I do so the temperature of the CHCl3 molecules drop down to almost 0K and the temperature of the peptide increases significantly. Has someone any experience with such a system and can give me a hint what to do? Thanks a lot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Antw: [gmx-users] multiple time step
Hallo, I would try to use the program protomol. There are many possibilities for performing multiple timestepping. Emanuel >>> oguz gurbulak 29.06.10 15.41 Uhr >>> Dear All, Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. Kind regards. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Antw: [gmx-users] multiple time step
Hi, I don't know what you aim to study, but consider the benefits and drawbacks of the programs and integration algorithms carefully if you want to use the multiple timestep algorithm to perform speedy calculations. More specifically: Is e.g NAMD with the multiple timestep algorithm really faster than gromacs with a uniform timestep? If you on the other hand want to compare integration schemes or something along those lines, then it's another matter of course. Erik Emanuel Peter skrev: Hallo, I would try to use the program protomol. There are many possibilities for performing multiple timestepping. Emanuel oguz gurbulak 29.06.10 15.41 Uhr >>> Dear All, Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. Kind regards. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: multiple time step
Chris, An interesting question... BTW, is there any philosophy of gromacs developers to avoid this algorithm in the MD engine? Vitaly > multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this. > > > -- original message -- > > Is it possible to carry out multiple time step molecular > dynamics simulations > in Gromacs > 4.0. versions ? Could you > please give me some information about this issue ? > > Thank you very much for your attention. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: multiple time step
Hi, The core developers have the answer for this one, but I can make an educated guess: Implementing it would mean a LOT of work and the rewards are small. The latter because most particles will have rougly the same oscillation period if one uses all-atom forcefields and turn on virtual sites and constrains the bonds, hence the point of having multiple time steps is lost. Vitaly Chaban skrev: Chris, An interesting question... BTW, is there any philosophy of gromacs developers to avoid this algorithm in the MD engine? Vitaly multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this. -- original message -- Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] ED sampling
Hi I need some information about how ED sampling works when a subset of the atoms are used for covariance analysis. Basically I would like to move the system along the first eigenvector obtained from covariance analysis of the C-alpha atoms only. From the paper "Toward an Exhaustive Sampling of the Configurational Spaces of two forms of the Peptide Hormone Guanylin" it appears only the C-alpha atoms are used to define the essential subspace but when I use the following commands, I get an error message saying: Fatal error: Nr of atoms in edsamp26-180fit.edi (4128) does not match nr of md atoms (294206) The commands are: tpbconv -s full180.tpr -f full180.trr -extend 5 -o edsam26-180f180.tpr -e full180.edr aprun -n 60 $GROMACS_DIR/bin/mdrun -s edsam26-180f180.tpr -nosum -o edsam26-180f180.trr -x edsam26-180f180.xtc -ei edsamp26-180fit.edi -c edsam26-180f180.gro -e edsam26-180f180.edr -g edsam26-180f180.log The ED sampling method I am using is linfix not radacc. Thanks Vijaya _ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Mixed Solvents Preparation?
Dear Gromas users, I want to run another set of MD simulation of my polymer in a mixed solvent. step 1 24 polymer molecules in a 10 * 10 * 10 nm of box. step 2 I want to add 50% (v/v) of two solvents to this box. I have already done an MD simulation with their individual solvents, now I want to run those polymers in their mixture. Please suggest? Rob -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Mixed Solvents Preparation?
tekle...@ualberta.ca wrote: Dear Gromas users, I want to run another set of MD simulation of my polymer in a mixed solvent. step 1 24 polymer molecules in a 10 * 10 * 10 nm of box. step 2 I want to add 50% (v/v) of two solvents to this box. I have already done an MD simulation with their individual solvents, now I want to run those polymers in their mixture. Please suggest? http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents -Justin Rob -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] REMD
Dear Justin, No dear I have not modelled the membrane, my protein is a simple protein which contained a loop about 59 amino acids. So I am intrested to model this loop through MD simulation. In this concerned I did 15 ns simulations, but right now don't know how to perform sampling for my protein (which is not a membrane, thermophilic or mesophilic protein) on same temperature i.e. 300k. In this regard is it correct to perform REMD, if yes then tell me how to perform it on single CPU? I am asking from you again to sure I can perform ot is it right to use REMD in my protein condition which in not a thermophilic protein. I think that REMD can only apply to those proteins which are thermophilic or mesophilic. please comment on this. Yes I wanted to sample loop dynamics, for which you have mentioned to run several simulations at the relevant (physiological?) temperature. Is it mean to run several (2,3,4..etc) diferent simulations at different time steps like 10ns, 15ns, 20ns, 30 ns etc. and analyze those results to obtain some averages from each and every simulations but it gives several averages values then how to sample all these simulations and finally how to get the average from these simulations. -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] REMD
pawan raghav wrote: Dear Justin, No dear I have not modelled the membrane, my protein is a simple protein which contained a loop about 59 amino acids. So I am intrested to model this loop through MD simulation. In this concerned I did 15 ns simulations, but right now don't know how to perform sampling for my protein (which is not a membrane, thermophilic or mesophilic protein) on same temperature i.e. 300k. In this regard is it correct to perform REMD, if yes then tell me how to perform it on single CPU? I am asking from you again to sure I can perform ot is it right to use REMD in my protein condition which in not a thermophilic protein. I think that REMD can only apply to those proteins which are thermophilic or mesophilic. please comment on this. REMD has nothing to do with whether or not the protein is thermophilic. Please do some background reading on the technique. You need multiple processors to run the simulation. The different replicates must be run concurrently so that they may periodically exchange. Since you are not modeling a membrane, I again wonder how you settled on the force field you did. Not that I think there's anything wrong with 53A6 (except for a bias towards extended structures, which you would have discovered with a bit of background reading). Just be prepared to justify your choice to a critical audience... Yes I wanted to sample loop dynamics, for which you have mentioned to run several simulations at the relevant (physiological?) temperature. Is it mean to run several (2,3,4..etc) diferent simulations at different time steps like 10ns, 15ns, 20ns, 30 ns etc. and analyze those results to obtain some averages from each and every simulations but it gives several averages values then how to sample all these simulations and finally how to get the average from these simulations. My suggestion was to run several simulations of equivalent length (such that the properties of interest converge) and obtain averages not only along each simulation, but also among all of them. -Justin -- Pawan -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Replicating monomer units
Hello Justin, I spent a full day to find a proper value for -d but it seems there is no way of getting correct bond lenght and angle at the same time. With the following commands I am getting correct bond length for the atoms connecting two monomer units but the angle is 140. I get 110 angle only when bond distance is much less than actual value (1.53 A). I have also tried monomer units with 6, 8, 10 carbon atoms. For 8 and 10 cases I can not even align carbons with the axis using princ. This proper geometry problem seems to be a very simple thing to figure out but I have reached no results. I would like you to provide me with a hint or suggestion...I appreciate your help. Thanks. Great Red Owns Many ACres of Sand 4 1Eth C11 0.462 0.285 0.269 1Eth C22 0.325 0.216 0.269 1Eth C33 0.213 0.321 0.269 1Eth C44 0.075 0.255 0.269 0.53817 0.53817 0.53817 editconf -f 4C.pdb -o 4Cd-princ.gro -princ -d 0.075 -bt cubic genconf -f 4Cd-princ.gro -o 4Cd-rep.gro -nbox 5 1 1 4Cd-rep.gro: replicated units: Great Red Owns Many ACres of Sand 20 1Eth C11 0.462 0.285 0.269 0. 0. 0. 1Eth C22 0.325 0.216 0.269 0. 0. 0. 1Eth C33 0.213 0.321 0.269 0. 0. 0. 1Eth C44 0.075 0.255 0.269 0. 0. 0. 2Eth C15 1.000 0.285 0.269 0. 0. 0. 2Eth C26 0.863 0.216 0.269 0. 0. 0. 2Eth C37 0.751 0.321 0.269 0. 0. 0. 2Eth C48 0.613 0.255 0.269 0. 0. 0. 3Eth C19 1.538 0.285 0.269 0. 0. 0. 3Eth C2 10 1.401 0.216 0.269 0. 0. 0. 3Eth C3 11 1.289 0.321 0.269 0. 0. 0. 3Eth C4 12 1.151 0.255 0.269 0. 0. 0. 4Eth C1 13 2.077 0.285 0.269 0. 0. 0. 4Eth C2 14 1.940 0.216 0.269 0. 0. 0. 4Eth C3 15 1.828 0.321 0.269 0. 0. 0. 4Eth C4 16 1.690 0.255 0.269 0. 0. 0. 5Eth C1 17 2.615 0.285 0.269 0. 0. 0. 5Eth C2 18 2.478 0.216 0.269 0. 0. 0. 5Eth C3 19 2.366 0.321 0.269 0. 0. 0. 5Eth C4 20 2.228 0.255 0.269 0. 0. 0. 2.69085 0.53817 0.53817 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Replicating monomer units
Moeed wrote: Hello Justin, I spent a full day to find a proper value for -d but it seems there is no way of getting correct bond lenght and angle at the same time. With the following commands I am getting correct bond length for the atoms connecting two monomer units but the angle is 140. I get 110 angle only when bond distance is much less than actual value (1.53 A). I have also tried monomer units with 6, 8, 10 carbon atoms. For 8 and 10 cases I can not even align carbons with the axis using princ. This proper geometry problem seems to be a very simple thing to figure out but I have reached no results. I would like you to provide me with a hint or suggestion...I appreciate your help. Thanks. There are two approaches. 1. Use a semi-correct geometry and run energy minimization to resolve any weird bonds/angles. 2. Orient your 4-carbon unit properly :) This requires special index groups for the structure you've generated. The 4-carbon unit is not changed when using editconf -princ. If you use this index file: [ special ] 1 3 [ all ] 1 2 3 4 Run: editconf -f C4.gro -o C4_princ.gro -n index.ndx -princ (Choose group 1 for determining the size, 0 for the orientation, and 1 for output) Then your structure is actually aligned perfectly with the x-axis. Using genconf should be simple at that point. A little bit of trigonometry will help you figure out the proper value of -d. If you still can't get that to work out, then approach #1 may work fine. -Justin Great Red Owns Many ACres of Sand 4 1Eth C11 0.462 0.285 0.269 1Eth C22 0.325 0.216 0.269 1Eth C33 0.213 0.321 0.269 1Eth C44 0.075 0.255 0.269 0.53817 0.53817 0.53817 editconf -f 4C.pdb -o 4Cd-princ.gro -princ -d 0.075 -bt cubic genconf -f 4Cd-princ.gro -o 4Cd-rep.gro -nbox 5 1 1 4Cd-rep.gro: replicated units: Great Red Owns Many ACres of Sand 20 1Eth C11 0.462 0.285 0.269 0. 0. 0. 1Eth C22 0.325 0.216 0.269 0. 0. 0. 1Eth C33 0.213 0.321 0.269 0. 0. 0. 1Eth C44 0.075 0.255 0.269 0. 0. 0. 2Eth C15 1.000 0.285 0.269 0. 0. 0. 2Eth C26 0.863 0.216 0.269 0. 0. 0. 2Eth C37 0.751 0.321 0.269 0. 0. 0. 2Eth C48 0.613 0.255 0.269 0. 0. 0. 3Eth C19 1.538 0.285 0.269 0. 0. 0. 3Eth C2 10 1.401 0.216 0.269 0. 0. 0. 3Eth C3 11 1.289 0.321 0.269 0. 0. 0. 3Eth C4 12 1.151 0.255 0.269 0. 0. 0. 4Eth C1 13 2.077 0.285 0.269 0. 0. 0. 4Eth C2 14 1.940 0.216 0.269 0. 0. 0. 4Eth C3 15 1.828 0.321 0.269 0. 0. 0. 4Eth C4 16 1.690 0.255 0.269 0. 0. 0. 5Eth C1 17 2.615 0.285 0.269 0. 0. 0. 5Eth C2 18 2.478 0.216 0.269 0. 0. 0. 5Eth C3 19 2.366 0.321 0.269 0. 0. 0. 5Eth C4 20 2.228 0.255 0.269 0. 0. 0. 2.69085 0.53817 0.53817 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] mdrun_mpi issue.
Hi Folks,
I am trying to run a simulation under GMX 4.0.5. When I do a qsub of my job, it
does not seem to run and gives me an error saying the library libimf.so is not
available. I tried subsequently giving/copying the library into the run path
with still the exact same error. I am attaching the .job file and error file
for your perusal. I d be glad for any ideas since I tried quite a few without
much help.
Thanks in advance
Rama
JOB FILE
*
#!/bin/bash
#PBS -l nodes=1:ppn=2
#PBS -l walltime=00:20:00
#PBS -j oe
#PBS -q debug
set -x
#move to my $SCRATCH directory
cd $SCRATCH
#RAMA STUFF ON WARHOL
#export PATH=$PATH:/usr/local/packages/gromacs4/bin/
#export PATH=$PATH:/usr/local/packages/intel/icc/11.0/074/lib/intel64/
exefile="/usr/local/packages/gromacs4/bin/mdrun_mpi"
projDir="MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes"
projName="4402_PR_0.5ns_Protein.tpr"
#copy executable to $SCRATCH
cp $HOME/${projDir}/${projName} ./
#cp /usr/local/packages/intel/icc/11.0/074/lib/intel64/libimf.so ./
#run my executable
mpirun ${exefile} -deffnm ${projName}
cp $SCRATCH/${projName}.* ${HOME}/${projDir}/*
***
ERROR FILE
***
+ cd /scratch/gullapal
+ exefile=/usr/local/packages/gromacs4/bin/mdrun_mpi
+ projDir=MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes
+ projName=4402_PR_0.5ns_Protein.tpr
+ cp
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_PR_0.5ns_Protein.tpr
./
+ mpirun /usr/local/packages/gromacs4/bin/mdrun_mpi -deffnm
4402_PR_0.5ns_Protein.tpr
/usr/local/packages/gromacs4/bin/mdrun_mpi: error while loading shared
libraries: libimf.so: cannot open shared object file: No s
uch file or directory
/usr/local/packages/gromacs4/bin/mdrun_mpi: error while loading shared
libraries: libimf.so: cannot open shared object file: No s
uch file or directory
+ cp '/scratch/gullapal/4402_PR_0.5ns_Protein.tpr.*'
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402
_nopep.job
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_PR_0.5ns_Protein.tpr
/usr/users/9/gullapa
l/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_pr_index.ndx
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_
Struc_PosRes/4402_topol.top
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/include_files
/usr/users/9/gu
llapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/pr.mdp
/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_
PosRes/Step1_nopep_Posre.gro
cp: target
`/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/Step1_nopep_Posre.gro'
is not a directory
--
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[gmx-users] Script for detecting interfaces
A couple of months ago someone mentioned a recent publication that went through a procedure for the detection of an interface / surface between phases for data from MD. Remember reading the publication and thinking was pretty neat and need to come back and try it. Well, for the life of me can't find it now, through my links, publication database, googling, literature search etc. Does anyone recall what it was or where I can find it? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] automating analysis using shell scripting
Dear Gromacs users, This question is much more of a linux shell scripting than of Gromacs. I have several distances to measure in my produced system for which I use g_dist. I need to shell script this so I don't have to set next to the machine while measuring those distances. The problem I face is that g_dist, and others like g_rms and g_rmsf, asks for input of the number of the group with or without an index file. My question is, how can I use shell scripting to answer those questions given by g_dist, giving it the number of the groups which is usually 0 an 1 using an index file of two atoms in the system? By doing this I can write a shell script of several g_dist lines, each is concerned with a specific distance, the shell script can input the number oif the groups to be measured, and I can do another experiment or go to the gym, or even cook something for dinner until it's done, lol Has anyone of you tried doing this? Thanks alot Hassan Shallal University of the Pacific Stockton, California From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Sat 6/26/2010 8:39 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 143 lloyd riggs wrote: > Dear (Justin too), > > Thank you for the replies. My main problem is lack of time, but I still have > the end of the proteins problem as of now. > > I only made the comment to justin partially as a joke, because he A) answeres > on averidge about 10-20 of these a day, seems too smart to be a help center, > and B) Every freind I have had in the past whom ends up overdoing on the help > BB (ie, CCP4, Phsics at CERN, etc...) ends up getting screwed in the end by > not balancing the "myself" getting my things done and making connections Vs. > Helping everyone else because they know so damned much about a specific > topic. All of my freinds in the similar situation started off looking about > as promissing, but then get ragged once they graduate, because everyone seems > to want a slave loyal to themselves as a post doc, before the professorship > is obtainable, etc...and end up writting video game software, hateing > academia for the way it really works Vs. the way it is supposed to work in > the scientific ideology we are taught at Universities and highschool. > > In any case, sorry to you Justin, I didn't mean to be such an ass. > Apology accepted. Please don't feel like you have to save me any trouble or look out for my productivity. I only reply to email when I really care to, and my comments are intended as helpful, not picky or overly critical :) I do appreciate this follow-up, as I have received several private emails telling me I'm a useless jerk, and they really do mean it... -Justin > Stephan Watkins > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] automating analysis using shell scripting
Hassan Shallal wrote: Dear Gromacs users, This question is much more of a linux shell scripting than of Gromacs. I have several distances to measure in my produced system for which I use g_dist. I need to shell script this so I don't have to set next to the machine while measuring those distances. The problem I face is that g_dist, and others like g_rms and g_rmsf, asks for input of the number of the group with or without an index file. My question is, how can I use shell scripting to answer those questions given by g_dist, giving it the number of the groups which is usually 0 an 1 using an index file of two atoms in the system? By doing this I can write a shell script of several g_dist lines, each is concerned with a specific distance, the shell script can input the number oif the groups to be measured, and I can do another experiment or go to the gym, or even cook something for dinner until it's done, lol Has anyone of you tried doing this? Yes, see here: http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin Thanks alot Hassan Shallal University of the Pacific Stockton, California From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Sat 6/26/2010 8:39 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 143 lloyd riggs wrote: Dear (Justin too), Thank you for the replies. My main problem is lack of time, but I still have the end of the proteins problem as of now. I only made the comment to justin partially as a joke, because he A) answeres on averidge about 10-20 of these a day, seems too smart to be a help center, and B) Every freind I have had in the past whom ends up overdoing on the help BB (ie, CCP4, Phsics at CERN, etc...) ends up getting screwed in the end by not balancing the "myself" getting my things done and making connections Vs. Helping everyone else because they know so damned much about a specific topic. All of my freinds in the similar situation started off looking about as promissing, but then get ragged once they graduate, because everyone seems to want a slave loyal to themselves as a post doc, before the professorship is obtainable, etc...and end up writting video game software, hateing academia for the way it really works Vs. the way it is supposed to work in the scientific ideology we are taught at Universities and highschool. In any case, sorry to you Justin, I didn't mean to be such an ass. Apology accepted. Please don't feel like you have to save me any trouble or look out for my productivity. I only reply to email when I really care to, and my comments are intended as helpful, not picky or overly critical :) I do appreciate this follow-up, as I have received several private emails telling me I'm a useless jerk, and they really do mean it... -Justin Stephan Watkins -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] automating analysis using shell scripting
Thanks Justin, this is just working amazingly From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Tue 6/29/2010 6:13 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] automating analysis using shell scripting Hassan Shallal wrote: > Dear Gromacs users, > > This question is much more of a linux shell scripting than of Gromacs. I have > several distances to measure in my produced system for which I use g_dist. I > need to shell script this so I don't have to set next to the machine while > measuring those distances. The problem I face is that g_dist, and others like > g_rms and g_rmsf, asks for input of the number of the group with or without > an index file. My question is, how can I use shell scripting to answer those > questions given by g_dist, giving it the number of the groups which is > usually 0 an 1 using an index file of two atoms in the system? > > By doing this I can write a shell script of several g_dist lines, each is > concerned with a specific distance, the shell script can input the number oif > the groups to be measured, and I can do another experiment or go to the gym, > or even cook something for dinner until it's done, lol > > Has anyone of you tried doing this? > Yes, see here: http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive -Justin > Thanks alot > Hassan Shallal > University of the Pacific > Stockton, California > > > > From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul > Sent: Sat 6/26/2010 8:39 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 143 > > > > > > lloyd riggs wrote: >> Dear (Justin too), >> >> Thank you for the replies. My main problem is lack of time, but I still have >> the end of the proteins problem as of now. >> >> I only made the comment to justin partially as a joke, because he A) answeres >> on averidge about 10-20 of these a day, seems too smart to be a help center, >> and B) Every freind I have had in the past whom ends up overdoing on the help >> BB (ie, CCP4, Phsics at CERN, etc...) ends up getting screwed in the end by >> not balancing the "myself" getting my things done and making connections Vs. >> Helping everyone else because they know so damned much about a specific >> topic. All of my freinds in the similar situation started off looking about >> as promissing, but then get ragged once they graduate, because everyone seems >> to want a slave loyal to themselves as a post doc, before the professorship >> is obtainable, etc...and end up writting video game software, hateing >> academia for the way it really works Vs. the way it is supposed to work in >> the scientific ideology we are taught at Universities and highschool. >> >> In any case, sorry to you Justin, I didn't mean to be such an ass. >> > > Apology accepted. Please don't feel like you have to save me any trouble or > look out for my productivity. I only reply to email when I really care to, > and > my comments are intended as helpful, not picky or overly critical :) I do > appreciate this follow-up, as I have received several private emails telling > me > I'm a useless jerk, and they really do mean it... > > -Justin > >> Stephan Watkins >> > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www inter
Re: [gmx-users] mdrun_mpi issue.
- Original Message -
From: quantrum75
Date: Wednesday, June 30, 2010 7:12
Subject: [gmx-users] mdrun_mpi issue.
To: gmx-users@gromacs.org
---
| > Hi Folks,
> I am trying to run a simulation under GMX 4.0.5. When I do a qsub of my job,
> it does not seem to run and gives me an error saying the library libimf.so is
> not available. I tried subsequently giving/copying the
If this installation used to work, then something's changed with the system
setup. Consult your sysadmins or compiler docs on how to set LD_LIBRARY_PATH
and/or LD_RUN_PATH environment variables so that run-time linking works like it
needs to. Or, set up fully static linking.
Mark
library into the run path with still the exact same error. I am attaching the
.job file and error file for your perusal. I d be glad for any ideas since I
tried quite a few without much help.
> Thanks in advance
> Rama
>
> JOB FILE
> *
>
> #!/bin/bash
> #PBS -l nodes=1:ppn=2
> #PBS -l walltime=00:20:00
> #PBS -j oe
> #PBS -q debug
>
>
> set -x
>
> #move to my $SCRATCH directory
> cd $SCRATCH
> #RAMA STUFF ON WARHOL
>
> #export PATH=$PATH:/usr/local/packages/gromacs4/bin/
> #export PATH=$PATH:/usr/local/packages/intel/icc/11.0/074/lib/intel64/
>
>
> exefile="/usr/local/packages/gromacs4/bin/mdrun_mpi"
> projDir="MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes"
> projName="4402_PR_0.5ns_Protein.tpr"
>
> #copy executable to $SCRATCH
> cp $HOME/${projDir}/${projName} ./
> #cp /usr/local/packages/intel/icc/11.0/074/lib/intel64/libimf.so ./
>
> #run my executable
> mpirun ${exefile} -deffnm ${projName}
> cp $SCRATCH/${projName}.* ${HOME}/${projDir}/*
>
>
> ***
> ERROR FILE
> ***
> + cd /scratch/gullapal
> + exefile=/usr/local/packages/gromacs4/bin/mdrun_mpi
> + projDir=MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes
> + projName=4402_PR_0.5ns_Protein.tpr
> + cp
> /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_PR_0.5ns_Protein.tpr
> ./
> + mpirun /usr/local/packages/gromacs4/bin/mdrun_mpi -deffnm
> 4402_PR_0.5ns_Protein.tpr
> /usr/local/packages/gromacs4/bin/mdrun_mpi: error while loading shared
> libraries: libimf.so: cannot open shared object file: No s
> uch file or directory
> /usr/local/packages/gromacs4/bin/mdrun_mpi: error while loading shared
> libraries: libimf.so: cannot open shared object file: No s
> uch file or directory
> + cp '/scratch/gullapal/4402_PR_0.5ns_Protein.tpr.*'
> /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402
> _nopep.job
> /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_PR_0.5ns_Protein.tpr
> /usr/users/9/gullapa
> l/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/4402_pr_index.ndx
> /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_
> Struc_PosRes/4402_topol.top
> /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/include_files
> /usr/users/9/gu
> llapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/pr.mdp
> /usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_
> PosRes/Step1_nopep_Posre.gro
> cp: target
> `/usr/users/9/gullapal/MHC/Structures/4402/nopeptide/Phase2_Struc_PosRes/Step1_nopep_Posre.gro'
> is not a directory
>
>
>
>
>
>
|
---
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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[gmx-users] REMD
Dear Justin, I have read manual there was an equation where T1 and T2 are the two temperatrure will be assign but in my case I don't have different temperature. I have to simulate at same temperature. Is there any other alternative to perform sampling rather than REMD. I am working on one processor so kindly suggest me the best for sampling. The force field which I have used was taken reference from paper. so please inform me if any thing wrong. -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] REMD
- Original Message - From: pawan raghav Date: Wednesday, June 30, 2010 14:56 Subject: [gmx-users] REMD To: gmx-users@gromacs.org > Dear Justin, > > I have read manual there was an equation where T1 and T2 > are the two temperatrure will be assign but in my case I don't have different > temperature. I have to simulate at same temperature. ... and if you'd read the accompanying text you'd understand why different temperatures are required. > Is there any other alternative to perform sampling rather than REMD. I am > working on one processor so kindly suggest me the best for sampling. REMD, coarse-graining, united-atom force fields, implicit solvation are all approaches that can be used to *enhance* the sampling per unit of computation, depending how you evaluate the inherent trade-offs. Some good textbook material will cover these ideas... > The force field which I have used was taken reference from paper. so please > inform me if any thing wrong. Judging that what others have done is suitable also for your case is something that only you can do. 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] multiple time step
I recall seeing something online about how gromacs developers have decided to focus on increasing the overall speed and allowing generally large timesteps (via e.g. angle constraints) vs. implementing multiple timestepping (no mailing list ref. sorry). I agree that this is not a logically exclusive decision -- PME takes >20% of the time so if they were doing it only 1/2 as often then there is the possibility of a real speedup. Nevertheless, it would need to be tested and perhaps the developers have indeed run these tests -- I've simply not seen the results. One would think, though, that PME could nearly always be done less often than, for example, bonded interactions. I agree with Erik that the work would be large, but I disagree that the benefits would be small -- although I suspect that neither of us has any data to support such claims :). Unfortunately, the bottom line is that this is free software and if you want it then you can code it. Or at the very least, you should benchmark the benefits on NAMD and then submit an "enhancement" bugzilla. Chris. -- original message -- The core developers have the answer for this one, but I can make an educated guess: Implementing it would mean a LOT of work and the rewards are small. The latter because most particles will have rougly the same oscillation period if one uses all-atom forcefields and turn on virtual sites and constrains the bonds, hence the point of having multiple time steps is lost. Vitaly Chaban skrev: Chris, An interesting question... BTW, is there any philosophy of gromacs developers to avoid this algorithm in the MD engine? Vitaly multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this. -- original message -- Is it possible to carry out multiple time step molecular dynamics simulations in Gromacs 4.0. versions ? Could you please give me some information about this issue ? Thank you very much for your attention. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
