Re: [Spam:*****] [gmx-users] REMD analysis
An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266
Re: [Spam:*****] [gmx-users] REMD analysis
Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63 .64 .64 .65 .65 .66 .66 Repl number of
Re: [Spam:*****] [gmx-users] REMD analysis
You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in the preference menu of grace. On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Repl .63 .63 .62 .62 .61 .61 .60 .60 .59 .59 .58 .59 .59 .60 .60 .61 .62 .62 .63
[gmx-users] Re: [gmx-developers] Wednesday, 15 May: upgrading redmine.gromacs.org
Hi, The new server is up and running. Let us know if you see issues. Cheers, Rossen On 5/12/13 8:56 PM, Rossen Apostolov wrote: Dear users and developers, On Wednesday the redmine server will be upgraded and moved to a new VM. Thus expect downtime of 1-2 hours (if it all goes well :-) ). Cheers, Rossen -- 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] Problems installing 4.6.1 on Mac 10.8.3
Hi I am unable to use cmake to install 4.6.1 on my macbook. I got cmake from macports, the version is 2.8.8. The command being used is: sudo cmake /Users/hkhandel/Downloads/gromacs-4.6.1/src/ Xcode and gcc are installed. The errors are something like this: CMake Error at gmxlib/CMakeLists.txt:120 (set_target_properties): set_target_properties called with incorrect number of arguments. CMake Error at gmxlib/CMakeLists.txt:123 (install): install TARGETS given no ARCHIVE DESTINATION for static library target gmx. etc. etc. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problems-installing-4-6-1-on-Mac-10-8-3-tp5008284.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] About AMBER Force field SB 2012 (ff12SB), using ACPYPE
With ACPYPE I can convert any Amber *.prmtop and *.crd to Gromacs, but it doesn't mean it will work straightforward (but I am working for that). For example, I am wondering how Gromacs team will port the Amber FF12SB, since now we have atom types like '2C', '3C' (ie. starting with a number), and GMX top won't accept this. Of course, a simple solution is to do '2C' - 'a2C' for example (and that works with grompp 4.6.1), but I am wondering what GMX developers would do here first, since using 3-letters wouldn't be a nice style. I am about to implement this workaround for ACPYPE, but just checking first if someone has a better idea/suggestion. Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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: [Spam:*****] [gmx-users] REMD analysis
Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ?? On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote: You need to increase the temperature gaps indeed if you want
Re: [gmx-users] Problems installing 4.6.1 on Mac 10.8.3
On 5/16/13 6:11 AM, khandelia wrote: Hi I am unable to use cmake to install 4.6.1 on my macbook. I got cmake from macports, the version is 2.8.8. The command being used is: sudo cmake /Users/hkhandel/Downloads/gromacs-4.6.1/src/ You shouldn't have to invoke sudo to do work in your own directory. You also should not be pointing to the src subdirectory of Gromacs. Please refer to the installation instructions online: http://www.gromacs.org/Documentation/Installation_Instructions -Justin Xcode and gcc are installed. The errors are something like this: CMake Error at gmxlib/CMakeLists.txt:120 (set_target_properties): set_target_properties called with incorrect number of arguments. CMake Error at gmxlib/CMakeLists.txt:123 (install): install TARGETS given no ARCHIVE DESTINATION for static library target gmx. etc. etc. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problems-installing-4-6-1-on-Mac-10-8-3-tp5008284.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Justin A. Lemkul, Ph.D. Research Scientist 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] coupling issue
Dear All, I have a system with two solutes (A and B) with water and ions. For pressure coupling in index file I defined two groups: Solute and Solvent, where solute consists of A+B and solvent consists of water+ions Due to some reasons I need to apply position restraints on Solute A only for few ns NPT run then make it free also. So while doing NPT run and using above said two groups in pressure coupling; that is Solute (A+B) and Solvent (water+ions) I get this Warning: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. Should I ignore this warning or do any of following: 1) Defining two groups: One with Solute A only and Second group with SoluteB+Water+ions 2) I am not sure which option I should use for refcoord_scaling option please suggest regards, JIom -- 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] coupling issue
On 5/16/13 8:12 AM, gromacs query wrote: Dear All, I have a system with two solutes (A and B) with water and ions. For pressure coupling in index file I defined two groups: Solute and Solvent, where solute consists of A+B and solvent consists of water+ions Due to some reasons I need to apply position restraints on Solute A only for few ns NPT run then make it free also. So while doing NPT run and using above said two groups in pressure coupling; that is Solute (A+B) and Solvent (water+ions) I get this Warning: You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option. Should I ignore this warning or do any of following: 1) Defining two groups: One with Solute A only and Second group with SoluteB+Water+ions The error arises due to pressure coupling, not temperature coupling. I don't think you necessarily need to split up the temperature coupling groups differently. 2) I am not sure which option I should use for refcoord_scaling option In almost all cases, use the 'com' setting for refcoord_scaling. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Reduced Units
Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- 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] REMD analysis
Indeed the Repeat-3 seems good. But I would guess you did not run too long, right! That would explain the distribution of values! On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png what could be wrong in this case?? Is it the mdp file settings or implicit solvent setting. Does the time to replica to exhange also affects their swapping ??
Re: [gmx-users] REMD analysis
Okay, now I can start with large production runs . On Thu, May 16, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote: Indeed the Repeat-3 seems good. But I would guess you did not run too long, right! That would explain the distribution of values! On May 16, 2013, at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well .
Re: [Spam:*****] [gmx-users] REMD analysis
On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? Probably. But exchange acceptance is a poor proxy for sampling efficiency - see recent discussions of REMD on this list. Mark So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are these showing all the replicas? what are the units? On May 14, 2013, at 5:07 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average probabilities: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .38 .43 .43 .36 .45 .40 .37 .48 .47 .45 .47 .44 .46 Repl number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl 50 42 46 52 57 40 58 49 42 53 61 63 56 57 58 Repl average number of exchanges: Repl 0123456789 10 11 12 13 14 15 Repl .40 .34 .37 .42 .46 .32 .46 .40 .34 .43 .49 .51 .45 .46 .46 Average acceptance ratio : 0.46 But, the repli_index.xvg and replica_temp.xvg files still shows that the replicas does not exchange equally well . https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png
Re: [gmx-users] Reduced Units
Does manual 2.3 help? On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- 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: [Spam:*****] [gmx-users] REMD analysis
Sorry to ask this simple question but how to read the replica_index and replica_temp files. I tried to search a lot but didn't find any information. As I have concatenated all log files and demuxed them. Here's first 10 lines from both files:- replica_index: 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456978 10 11 12 6 1023459678 10 11 12 8 1203495768 10 11 12 10 1230947568 11 10 12 replica_temp 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456897 10 11 12 6 1023457896 10 11 12 8 2013468795 10 11 12 10 3012578694 11 10 12 On Thu, May 16, 2013 at 11:24 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? Probably. But exchange acceptance is a poor proxy for sampling efficiency - see recent discussions of REMD on this list. Mark So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I proceed for large production runs to complete my experiment ?? On Tue, May 14, 2013 at 6:34 PM, XAvier Periole x.peri...@rug.nl wrote: The interval between the exchange trial affect the efficiency of REMD but not the the exchange ratio (at least in principle). In you case I am not sure what the plot are showing! Are
Re: [Spam:*****] [gmx-users] REMD analysis
They show which structure is in which ensemble, and the inverse. Look at the exchange events reported in the .log files and work out which is which. Mark On Thu, May 16, 2013 at 5:25 PM, bharat gupta bharat.85.m...@gmail.comwrote: Sorry to ask this simple question but how to read the replica_index and replica_temp files. I tried to search a lot but didn't find any information. As I have concatenated all log files and demuxed them. Here's first 10 lines from both files:- replica_index: 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456978 10 11 12 6 1023459678 10 11 12 8 1203495768 10 11 12 10 1230947568 11 10 12 replica_temp 0 0123456789 10 11 12 2 1023456798 10 11 12 4 1023456897 10 11 12 6 1023457896 10 11 12 8 2013468795 10 11 12 10 3012578694 11 10 12 On Thu, May 16, 2013 at 11:24 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Here's the result of three different runs : Temperature distribution for three trials Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627 Repeat-2 280 299 319 340 363 388 414 441 471 503 536 572 611 Repeat-3 280 300 322 345 370 397 426 457 490 526 564 605 649 md.log files output from three different trials: Repeat-1 .37 .28 .26 .30 .25 .29 .32 .35 .32 .35 .36 .32 .31 Repeat-2 .30 .33 .30 .25 .19 .27 .30 .31 .27 .40 .34 .31 Repeat-3 .18 .22 .26 .34 .26 .28 .25 .27 .27 .25 .27 .22 I think as the required acceptance value all the three trials are fine, but trail 3 would be much better to continue the further runs and anlysis ?? Probably. But exchange acceptance is a poor proxy for sampling efficiency - see recent discussions of REMD on this list. Mark So, is it fine to continue with the third simulation ?? But still the problem is that I am not getting the exact graphs with xmgrace?? On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote: You have to convince yourself, not me :)) But I can give you my opinion … On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote: Okay Sir, I will try two-three combinations this time and will report back to you ... On Thu, May 16, 2013 at 5:25 PM, XAvier Periole x.peri...@rug.nl wrote: An acceptance ratio of 0.2/0.3 is normally best. The problem with high acceptance ratio is that it means that a large portion of the exchanges are just back and forth exchanges between consecutive exchange and are thus disturbing the system more that actually helping sampling. I do not know particularly the paper you mention but if you like what they do, it is your choice at the end. Why don;t you just increase the spacing between the replicas? You will need less replicas and potentially you could run two simulations instead of one and evaluate the convergence ... On May 16, 2013, at 1:50 AM, bharat gupta bharat.85.m...@gmail.com wrote: The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica_temp.bmp https://www.dropbox.com/s/8jfs0b9whu6j7lo/replica_index.bmp Now regarding the high acceptance ratio which is 0.5 , I came across a paper (http://www.pnas.org/content/100/13/7587.full.pdf), here they have mentioned that their average acceptance ratio ranged between 30 to 80%. I have a question here, how did they calculate the range for the average acceptance ratio or is it average ratio for each replica . Actually, this is the reference I am following. I am also interested in peptide folding simulation, similar to this article. I want to know, whether the average acceptance ratio that I have got for my trial simulation is correct , together with the replica_temp and replica_remd plots. Can I
Re: [gmx-users] About AMBER Force field SB 2012 (ff12SB), using ACPYPE
On Thu, May 16, 2013 at 12:37 PM, Alan alanwil...@gmail.com wrote: With ACPYPE I can convert any Amber *.prmtop and *.crd to Gromacs, but it doesn't mean it will work straightforward (but I am working for that). For example, I am wondering how Gromacs team will port the Amber FF12SB, There's no plan to do so, but if someone wants to do so and can demonstrate they've done it correctly (e.g. suitable agreement with the native version) then contributions are always welcome. since now we have atom types like '2C', '3C' (ie. starting with a number), and GMX top won't accept this. What is the specific issue? Of course, a simple solution is to do '2C' - 'a2C' for example (and that works with grompp 4.6.1), but I am wondering what GMX developers would do here first, since using 3-letters wouldn't be a nice style. Offhand, I can't think of a good reason to require an atom type to start with a letter, but there are a lot of hidden gotchas about how GROMACS parse lots of ugly file formats under lots of conditions... I am about to implement this workaround for ACPYPE, but just checking first if someone has a better idea/suggestion. Seems OK to me, offhand, but I don't have anything like full information, or time to get it :-( Mark Alan -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- 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] Performance (GMX4.6.1): MPI vs Threads
Dear all, if one performs a parallel calculation on a single node / computer with more than 1 core, is there a speed difference between MPI and Threads? Problem is for gromacs 4.6.1 i'm facing problems to link it to OpenMpi. A serial version (without threads) worked, so i think i should be able to compile a version which supports threads. Since we only run calculations on a single node on our cluster (no infini-band), i'm wondering if the programm with threads would be sufficient in our case. Greetings Thomas -- 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] Performance (GMX4.6.1): MPI vs Threads
cmake -DGMX_THREAD_MPI=on is intended to provide maximum performance for your case, i.e. a single node. It's on by default for a reason ;-) Mark On Thu, May 16, 2013 at 6:57 PM, Thomas Schlesier schl...@uni-mainz.dewrote: Dear all, if one performs a parallel calculation on a single node / computer with more than 1 core, is there a speed difference between MPI and Threads? Problem is for gromacs 4.6.1 i'm facing problems to link it to OpenMpi. A serial version (without threads) worked, so i think i should be able to compile a version which supports threads. Since we only run calculations on a single node on our cluster (no infini-band), i'm wondering if the programm with threads would be sufficient in our case. Greetings Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Performance (GMX4.6.1): MPI vs Threads
I'm not sure what you mean by threads. In GROMACS this can refer to either thread-MPI or OpenMP multi-threading. To run within a single compute node a default GROMACS installation using either of the two aforementioned parallelization methods (or a combination of the two) can be used. -- Szilárd On Thu, May 16, 2013 at 6:57 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Dear all, if one performs a parallel calculation on a single node / computer with more than 1 core, is there a speed difference between MPI and Threads? Problem is for gromacs 4.6.1 i'm facing problems to link it to OpenMpi. A serial version (without threads) worked, so i think i should be able to compile a version which supports threads. Since we only run calculations on a single node on our cluster (no infini-band), i'm wondering if the programm with threads would be sufficient in our case. Greetings Thomas -- 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] Performance (GMX4.6.1): MPI vs Threads
PS: if your compute-nodes are Intel of some recent architecture OpenMP-only parallelization can be considerably more efficient. For more details see http://www.gromacs.org/Documentation/Acceleration_and_parallelization -- Szilárd On Thu, May 16, 2013 at 7:26 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: I'm not sure what you mean by threads. In GROMACS this can refer to either thread-MPI or OpenMP multi-threading. To run within a single compute node a default GROMACS installation using either of the two aforementioned parallelization methods (or a combination of the two) can be used. -- Szilárd On Thu, May 16, 2013 at 6:57 PM, Thomas Schlesier schl...@uni-mainz.de wrote: Dear all, if one performs a parallel calculation on a single node / computer with more than 1 core, is there a speed difference between MPI and Threads? Problem is for gromacs 4.6.1 i'm facing problems to link it to OpenMpi. A serial version (without threads) worked, so i think i should be able to compile a version which supports threads. Since we only run calculations on a single node on our cluster (no infini-band), i'm wondering if the programm with threads would be sufficient in our case. Greetings Thomas -- 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] gmx 4.6 does not detect GPUs, but 4.5 does
Dear all, I have just updated the GROMACS installation at a local cluster which have 2 GPUs. I installed CUDA 5 with no problems and it was detected by cmake. No problems during installation. With GROMACS 4.5 I was able to use the GPUs of this same cluster, but now GROMACS 4.6 says that it can't detect the GPUs: when I use -gpu_id 01 (0 and 1 were the IDs I used before) , -gpu_id 0 or -gpu_id 1: Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: without -gpu_id, but with -nb gpu : Fatal error: GPU acceleration requested, but no compatible GPUs were detected. I searched the list but couldn't find anything about this particular case. Am I doing something wrong? Do I need to activate CUDA or something like this? The CUDA version which GROMACS 4.5 was using is 3.1 Any ideas about how could I solve this? thanks in advance, Leandro -- 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] point in source code to access atom position
Hi I want to store Z coordinates of atoms at the beginning of each time step when I am doing 'mdrun -rerun'. I am not able to find the line and file in the source code where I can implement this. Can anyone please help me with that? Thanks Sikandar -- 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] gmx 4.6 does not detect GPUs, but 4.5 does
On 5/16/13 9:14 PM, Leandro Bortot wrote: Dear all, I have just updated the GROMACS installation at a local cluster which have 2 GPUs. I installed CUDA 5 with no problems and it was detected by cmake. No problems during installation. With GROMACS 4.5 I was able to use the GPUs of this same cluster, but now GROMACS 4.6 says that it can't detect the GPUs: when I use -gpu_id 01 (0 and 1 were the IDs I used before) , -gpu_id 0 or -gpu_id 1: Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: without -gpu_id, but with -nb gpu : Fatal error: GPU acceleration requested, but no compatible GPUs were detected. I searched the list but couldn't find anything about this particular case. Am I doing something wrong? Do I need to activate CUDA or something like this? The CUDA version which GROMACS 4.5 was using is 3.1 Any ideas about how could I solve this? What are the GPU cards? Do they meet the minimum requirements for Gromacs' native 4.6 GPU acceleration? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Running Pull Code
Hi, I have a system composed of POPC/peptide/water/ions. I aim to study ion conduction through the peptide using umbrella sampling. I built the system and ran EM, NVT, NPT successfully, but have not run md yet. I' d like to know if the system is required of passing a few nanoseconds md? Or I might be able to go to Umbrella Sampling straight after NPT? As I studied in Justin's tutorial, running pull code is done after some typical steps of every simulation ( EM, NVT, NPT). But I dont know if is correct generally for other systems as well? Would you please give me any suggestions? Thanks in advance. Sincerely, Shima -- 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] Interaction spectra of inhibitor–residue pair in the protein–inhibitor complexes
Respected sir Which command do we use to determine Interaction spectra of inhibitor–residue pair in the protein–inhibitor complexes as we have g_hbond to determine the hydrogen bond between protein and ligand -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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] point in source code to access atom position
Do you need it in the code? g_traj would help you do that on the trajectory. On May 17, 2013, at 3:17 AM, Sikandar Mashayak symasha...@gmail.com wrote: Hi I want to store Z coordinates of atoms at the beginning of each time step when I am doing 'mdrun -rerun'. I am not able to find the line and file in the source code where I can implement this. Can anyone please help me with that? Thanks Sikandar -- 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] Reduced Units
Are you sure lattice cell set up in f.c.c structure has been explained there for the positions of molecules? On Thu, May 16, 2013 at 3:28 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Does manual 2.3 help? On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com wrote: Hi All, Has anyone performed MD simulation on fluids in reduced units with GROMACS? I just wandering how the obtained density values through the box should be converted in the SI unit (Kg/m3). Thanks Rasoul -- 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
