Re: [gmx-users] CHARMM36 force field available for GROMACS
Dear Justin, Thanks for you information. I have a small query on the residue name in the charmm36.ff folder. Is there any document illustrating for the corresponding full name of residues in the .rtp file. As you have illustrated in the file forcefield.doc, the parameters for some carbohydrates such as glucose should be implemented. I found the residues named AALT or AALL should be for glucose, but the names are not easy to understand. Is there any illustration already existing to explain what the abbreviations stand for? Pan 2013/10/9 rajat desikan rajatdesi...@gmail.com Superb stuff, Justin. Thank you so much. Is it asking too much for a brief list of the test systems that you used? Thanks again. On Wed, Oct 9, 2013 at 1:46 AM, Justin Lemkul jalem...@vt.edu wrote: All, I am pleased to announce the immediate availability of the latest CHARMM36 force field in GROMACS format. You can obtain the archive from our lab's website at http://mackerell.umaryland.**edu/CHARMM_ff_params.html http://mackerell.umaryland.edu/CHARMM_ff_params.html . The present version contains up-to-date parameters for proteins, nucleic acids, lipids, some carbohydrates, CGenFF version 2b7, and a variety of of other small molecules. Please refer to forcefield.doc, which contains a list of citations that describe the parameters, as well as the CHARMM force field files that were used to generate the distribution. We have validated the parameters by comparing energies of a wide variety of molecules within CHARMM and GROMACS and have found excellent agreement between the two. If anyone has any issues or questions, please feel free to post them to this list or directly to me at the email address below. Happy simulating! -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://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_Lists http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 -- Pan Chen CERMAV-CNRS BP 53 38041 Grenoble Cedex 9 tel. +33 (0)4 76 03 76 12 fax. +33 (0)4 76 54 72 03 -- 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] g_hbond
Hi Maggin, The middle column is the total number of hydrogen bonds in your system under the definition of the hydrogen bonds criteria you have defined (here you used the default value). The third column is the number of acceptor-donor paris in the system. The first column is the simulation time, your trajectory file are saved every 2 ps right? If you use xmgrace bovin_hnum.xvg, you can easily find what's the meaning of the second and third column. Pan 2013/5/24 maggin maggin.c...@gmail.com # This file was created Fri May 24 13:03:14 2013 # by the following command: # g_hbond -f traj_all_md.trr -s md_0_1_next1.tpr -num bovin_hnum.xvg # # g_hbond is part of G R O M A C S: # # Green Red Orange Magenta Azure Cyan Skyblue # @title Hydrogen Bonds @xaxis label Time (ps) @yaxis label Number @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 74 517 2 73 515 4 69 515 6 69 529 8 78 525 10 74 517 12 68 516 14 68 524 16 71 520 hi, anybody can tell me at here if Hydrogen bonds Refers to the middle column: 74,73,69,69,78,74,68,68,71 Thank you ! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507.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 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] the -dist flag of g_hbond tool
Dear Gromacs users, I am confused about the g_hbond tools. 1) When I use -dist to get the distribution of hydrogen bonding distance, I found that the summation of the population is always 200 (the y-column below). I am not sure if it's was done with normalization or not, if yes, the summation should be one, if no, then the summation should equals to the total number of the hydrogen bonds, but here the hbnum.xvg shows me I have 440 hydrogen bonds. Why here is always 200, not matter what types of hydrogen bonds. 2) In my system, there are several different types of hydrogen bonds, such as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen bonds. Is there any smart way to separately calculate those hydrogen bonds? By using the index.ndx file, I could separate the intra-chain hydrogen bonds, then I can get the inter-chain ones using the total one minus the intra-chain one. It may be possible to do the same for the intra-sheet and the inter-sheet. However, this strategy seems complex. Did anybody have experience or ideas for this problem? Pan # This file was created Fri May 24 11:06:01 2013 # by the following command: # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000 -e 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g # # g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title Hydrogen Bond Distribution @xaxis label Hydrogen - Acceptor Distance (nm) @yaxis label @TYPE xy 0.0025 0 0.0075 0 0.0125 0 0.0175 0 0.0225 0 0.0275 0 0.0325 0 0.0375 0 0.0425 0 0.0475 0 0.0525 0 0.0575 0 0.0625 0 0.0675 0 0.0725 0 0.0775 0 0.0825 0 0.0875 0 0.0925 0 0.0975 0 0.1025 0 0.1075 0 0.1125 0 0.1175 0 0.1225 0 0.1275 0 0.1325 0 0.1375 0 0.1425 0 0.1475 0 0.1525 0 0.1575 0 0.1625 0 0.1675 0 0.1725 0 0.1775 0 0.1825 0 0.1875 0 0.1925 0 0.1975 0 0.2025 0 0.2075 0 0.2125 0 0.2175 0 0.2225 0 0.2275 0 0.2325 0.00538632 0.2375 0.125501 0.24251.23562 0.24756.08295 0.252516.4279 0.257528.6597 0.262536.0576 0.2675 35.154 0.272528.1539 0.277519.8073 0.282512.4602 0.28757.23832 0.29254.06577 0.29752.15794 0.30251.14423 0.3075 0.588366 0.3125 0.310611 0.3175 0.163206 0.3225 0.0772039 0.3275 0.0411156 0.3325 0.0210066 0.3375 0.0113113 0.3425 0.00574541 0.3475 0.00502723 -- 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] the -dist flag of g_hbond tool
Hi, I have 512 donors and 1024 acceptors. I have just tested g_hbond with my standard crystal structure, which I should get 512 hydrogen bonds. And the output hbnum.xvg does show 512 hydrogen bonds, which is correct. But the hbdist.xvg file still shows that the summation of population is 200. 2013/5/24 Erik Marklund er...@xray.bmc.uu.se Hi, See below On 24 May 2013, at 11:45, CHEN Pan evan.pan.c...@gmail.com wrote: Dear Gromacs users, I am confused about the g_hbond tools. 1) When I use -dist to get the distribution of hydrogen bonding distance, I found that the summation of the population is always 200 (the y-column below). I am not sure if it's was done with normalization or not, if yes, the summation should be one, if no, then the summation should equals to the total number of the hydrogen bonds, but here the hbnum.xvg shows me I have 440 hydrogen bonds. Why here is always 200, not matter what types of hydrogen bonds. How many donors do you have, and how many acceptors? 2) In my system, there are several different types of hydrogen bonds, such as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen bonds. Is there any smart way to separately calculate those hydrogen bonds? By using the index.ndx file, I could separate the intra-chain hydrogen bonds, then I can get the inter-chain ones using the total one minus the intra-chain one. It may be possible to do the same for the intra-sheet and the inter-sheet. However, this strategy seems complex. Did anybody have experience or ideas for this problem? Pan # This file was created Fri May 24 11:06:01 2013 # by the following command: # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000 -e 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g # # g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title Hydrogen Bond Distribution @xaxis label Hydrogen - Acceptor Distance (nm) @yaxis label @TYPE xy 0.0025 0 0.0075 0 0.0125 0 0.0175 0 0.0225 0 0.0275 0 0.0325 0 0.0375 0 0.0425 0 0.0475 0 0.0525 0 0.0575 0 0.0625 0 0.0675 0 0.0725 0 0.0775 0 0.0825 0 0.0875 0 0.0925 0 0.0975 0 0.1025 0 0.1075 0 0.1125 0 0.1175 0 0.1225 0 0.1275 0 0.1325 0 0.1375 0 0.1425 0 0.1475 0 0.1525 0 0.1575 0 0.1625 0 0.1675 0 0.1725 0 0.1775 0 0.1825 0 0.1875 0 0.1925 0 0.1975 0 0.2025 0 0.2075 0 0.2125 0 0.2175 0 0.2225 0 0.2275 0 0.2325 0.00538632 0.2375 0.125501 0.24251.23562 0.24756.08295 0.252516.4279 0.257528.6597 0.262536.0576 0.2675 35.154 0.272528.1539 0.277519.8073 0.282512.4602 0.28757.23832 0.29254.06577 0.29752.15794 0.30251.14423 0.3075 0.588366 0.3125 0.310611 0.3175 0.163206 0.3225 0.0772039 0.3275 0.0411156 0.3325 0.0210066 0.3375 0.0113113 0.3425 0.00574541 0.3475 0.00502723 -- 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 -- Pan Chen CERMAV-CNRS BP 53 38041 Grenoble Cedex 9 tel. +33 (0)4 76 03 76 12 fax. +33 (0)4 76 54 72 03 -- 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
Re: [gmx-users] the -dist flag of g_hbond tool
Yes. I have looked at it already. I may need to spend time to understand it. By the way, in the source code, it seems some part are written for calculating hydrogen bonding energy, but I haven't see any flag command could give a output of hydrogen bonding energy file. Is it still under development? 2013/5/24 Erik Marklund er...@xray.bmc.uu.se Hm. That is peculiar. The source code has the answer of course. I can have a look next week to see why that is. Erik On 24 May 2013, at 14:11, CHEN Pan evan.pan.c...@gmail.com wrote: Hi, I have 512 donors and 1024 acceptors. I have just tested g_hbond with my standard crystal structure, which I should get 512 hydrogen bonds. And the output hbnum.xvg does show 512 hydrogen bonds, which is correct. But the hbdist.xvg file still shows that the summation of population is 200. 2013/5/24 Erik Marklund er...@xray.bmc.uu.se Hi, See below On 24 May 2013, at 11:45, CHEN Pan evan.pan.c...@gmail.com wrote: Dear Gromacs users, I am confused about the g_hbond tools. 1) When I use -dist to get the distribution of hydrogen bonding distance, I found that the summation of the population is always 200 (the y-column below). I am not sure if it's was done with normalization or not, if yes, the summation should be one, if no, then the summation should equals to the total number of the hydrogen bonds, but here the hbnum.xvg shows me I have 440 hydrogen bonds. Why here is always 200, not matter what types of hydrogen bonds. How many donors do you have, and how many acceptors? 2) In my system, there are several different types of hydrogen bonds, such as intra-chain and inter-chain or intra-sheet and inter-sheet hydrogen bonds. Is there any smart way to separately calculate those hydrogen bonds? By using the index.ndx file, I could separate the intra-chain hydrogen bonds, then I can get the inter-chain ones using the total one minus the intra-chain one. It may be possible to do the same for the intra-sheet and the inter-sheet. However, this strategy seems complex. Did anybody have experience or ideas for this problem? Pan # This file was created Fri May 24 11:06:01 2013 # by the following command: # g_hbond -f /Users/panchen/gromacs.file/ch1-56/alpha/md-a-re.xtc -s /Users/panchen/gromacs.file/ch1-56/alpha/md-a.tpr -n ../ful.ndx -b 11000 -e 16000 -a 30 -r 0.35 -da -num -hbn -ang -dist -g # # g_hbond is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title Hydrogen Bond Distribution @xaxis label Hydrogen - Acceptor Distance (nm) @yaxis label @TYPE xy 0.0025 0 0.0075 0 0.0125 0 0.0175 0 0.0225 0 0.0275 0 0.0325 0 0.0375 0 0.0425 0 0.0475 0 0.0525 0 0.0575 0 0.0625 0 0.0675 0 0.0725 0 0.0775 0 0.0825 0 0.0875 0 0.0925 0 0.0975 0 0.1025 0 0.1075 0 0.1125 0 0.1175 0 0.1225 0 0.1275 0 0.1325 0 0.1375 0 0.1425 0 0.1475 0 0.1525 0 0.1575 0 0.1625 0 0.1675 0 0.1725 0 0.1775 0 0.1825 0 0.1875 0 0.1925 0 0.1975 0 0.2025 0 0.2075 0 0.2125 0 0.2175 0 0.2225 0 0.2275 0 0.2325 0.00538632 0.2375 0.125501 0.24251.23562 0.24756.08295 0.252516.4279 0.257528.6597 0.262536.0576 0.2675 35.154 0.272528.1539 0.277519.8073 0.282512.4602 0.28757.23832 0.29254.06577 0.29752.15794 0.30251.14423 0.3075 0.588366 0.3125 0.310611 0.3175 0.163206 0.3225 0.0772039 0.3275 0.0411156 0.3325 0.0210066 0.3375 0.0113113 0.3425 0.00574541 0.3475 0.00502723 -- 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
