Re: [gmx-users] itp atomtypes section
Hi James, The 6 and 1 are the number of electrons the atomtype has, which is used for QM/MM stuff. Gromacs can tell whether or not it is given by checking the format of the line. If the 5th column is a letter, then the number isn't there, if the 6th column is a letter, it must be there. Hope it helps, Tsjerk On Tue, Nov 27, 2012 at 3:45 AM, James Cannon jamesresearch...@gmail.comwrote: Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF HF 1 1.008000.1000 A3.5e-01 4.28529e-01 I can't work out what the column containing the 6 and 1 is for. Can anyone help? It's not documented anywhere that I can find. 2. I notice that there are many types of atomtypes fields. From the manual: [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 This is clearly a different format to my sample above. Why does the format vary? I know the above format is not wrong because it runs succcessfully in a test-run. How does gromacs know which format to use correctly? I appreciate any help. Thank you. Best regards, James -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] error during minimization
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization (after shrinking), getting error like this. Fatal error: Invalid line in system_shrink26.gro for atom 8703: 6.4140 6.44350 6.59650.why this error?plz give me a solution to overcome it. -- 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] error during minimization
Probably..there is a problem in spacing at the bottom of your gro file. The line mentioning the vectors should be like this eg:, 5012OBC49 47 1.088 1.094 2.775 0.0 0.0 0.0 On Tue, Nov 27, 2012 at 3:01 PM, Shine A shin...@iisertvm.ac.in wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization (after shrinking), getting error like this. Fatal error: Invalid line in system_shrink26.gro for atom 8703: 6.4140 6.44350 6.59650.why this error?plz give me a solution to overcome it. -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] error during minimization
On 11/27/12 4:31 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization (after shrinking), getting error like this. Fatal error: Invalid line in system_shrink26.gro for atom 8703: 6.4140 6.44350 6.59650.why this error?plz give me a solution to overcome it. The program is complaining that it is looking for an atom and finding box vectors. That indicates a mismatch between the number of atoms (specified on the second line of the .gro file) and the actual number of atoms. -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
Re: [gmx-users] g_select error
hello Justin: thanks for kind tips. I've tried both methods: g_select -f md.xtc -s npt3.pdb -os size.xvg -sf selection.dat g_select -f md.xtc -s npt3.pdb -os size.xvg -select 'resname SOL and name OW within 0.6 of resid 114' but they all failed with messages: log WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resname SOL and name OW within 0.6 of resid 114' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Yeah, a Wuzz, Or a Jerk (F. Black) On 11/27/2012 01:54 AM, Justin Lemkul wrote: On 11/26/12 2:08 PM, Albert wrote: hello: I am going to calculate the number of water molecules within 6 A of residue 114 by following command: g_select -f md.xtc -s npt3.pdb -os size.xvg -select resid 114 and rdist 0.6 but it said: WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resid 114 and rdist 0.6' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- You haven't defined rdist to actually be anything. If you need to be using multi-line selections, you should be providing a selection.dat file to -sf instead of using single-line statements to -select. Something like g_select -select 'resname SOL and name OW within 0.6 of resid 114' should do the trick, but I haven't actually tried that so I'm not 100% sure. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_select error
On 11/27/12 9:18 AM, Albert wrote: hello Justin: thanks for kind tips. I've tried both methods: g_select -f md.xtc -s npt3.pdb -os size.xvg -sf selection.dat g_select -f md.xtc -s npt3.pdb -os size.xvg -select 'resname SOL and name OW within 0.6 of resid 114' but they all failed with messages: log WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. selection parser: syntax error selection parser: invalid selection 'resname SOL and name OW within 0.6 of resid 114' --- Program g_select, VERSION 4.5.5 Source code file: trajana.c, line: 1310 Input error or input inconsistency: selection(s) could not be parsed For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Well, like I warned, I wasn't 100% sure of the syntax, so it was no guarantee that I was right. Reading into the documentation and examples a bit, it seems that resname SOL and name OW should be enclosed within double quotes, within the single-quoted string. Otherwise, use this selection.dat file: waterO = name OW; close = waterO and within 0.6 of resid 114; close; It should be possible to do it in one line, but the above set of selections seems to work fine. -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
Re: [gmx-users] g_select error
On 11/27/2012 03:33 PM, Justin Lemkul wrote: Well, like I warned, I wasn't 100% sure of the syntax, so it was no guarantee that I was right. Reading into the documentation and examples a bit, it seems that resname SOL and name OW should be enclosed within double quotes, within the single-quoted string. Otherwise, use this selection.dat file: waterO = name OW; close = waterO and within 0.6 of resid 114; close; It should be possible to do it in one line, but the above set of selections seems to work fine. -Justin thank you so much for such kind helps. it finally works.;-) best Albert -- 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] g_bar and second law violations
Hi, I am trying to compute the free energy change using g_bar: I am using two-stage decoupling process as in Justin Lemkul's tutorial. But , I get following warning in all cases regarding violation of second law of thermodynamics. Can someone explain what is this error about and which lambda I should look for? Here is the output. Detailed results in kT (see help for explanation): lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0.000 0.100 -0.39 0.08 -0.64 0.06 -0.09 0.20 0.88 0.05 0.100 0.150 0.08 0.04 0.07 0.03 0.09 0.05 0.43 0.01 0.150 0.200 0.12 0.02 -0.11 0.03 0.36 0.06 0.54 0.02 0.200 0.300 0.54 0.06 -0.05 0.07 1.25 0.15 1.24 0.03 0.300 0.350 0.21 0.03 0.15 0.04 0.31 0.06 0.72 0.01 0.350 0.400 -0.01 0.02 0.11 0.03 -0.08 0.04 0.64 0.01 0.400 0.500 -0.37 0.03 0.22 0.02 -0.78 0.06 1.07 0.01 0.500 0.600 -0.58 0.01 0.17 0.04 -1.17 0.04 0.99 0.01 0.600 0.700 -0.74 0.03 0.16 0.02 -1.51 0.07 0.89 0.01 0.700 0.750 -0.37 0.01 -0.02 0.02 -0.69 0.03 0.47 0.01 0.750 0.800 -0.26 0.01 -0.07 0.01 -0.42 0.02 0.53 0.01 0.800 0.850 -0.19 0.01 0.03 0.01 -0.38 0.03 0.57 0.01 0.850 0.900 -0.24 0.02 0.06 0.01 -0.50 0.04 0.58 0.01 0.900 1.000 -0.47 0.07 -0.04 0.05 -0.12 0.34 1.13 0.06 WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations. Final results in kJ/mol: lambda 0.000 - 0.100, DG -0.97 +/- 0.19 lambda 0.100 - 0.150, DG 0.20 +/- 0.09 lambda 0.150 - 0.200, DG 0.30 +/- 0.05 lambda 0.200 - 0.300, DG 1.34 +/- 0.15 lambda 0.300 - 0.350, DG 0.52 +/- 0.07 lambda 0.350 - 0.400, DG -0.02 +/- 0.05 lambda 0.400 - 0.500, DG -0.92 +/- 0.08 lambda 0.500 - 0.600, DG -1.45 +/- 0.03 lambda 0.600 - 0.700, DG -1.86 +/- 0.08 lambda 0.700 - 0.750, DG -0.91 +/- 0.03 lambda 0.750 - 0.800, DG -0.64 +/- 0.03 lambda 0.800 - 0.850, DG -0.48 +/- 0.03 lambda 0.850 - 0.900, DG -0.61 +/- 0.04 lambda 0.900 - 1.000, DG -1.17 +/- 0.18 total 0.000 - 1.000, DG -6.68 +/- 0.30 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to run charmm2gromacs-pvm.py correctly?
Hello: I am trying to convert the output from CGenFF website into Gromacs .itp format by command: python charmm2gromacs-pvm.py charmm.rst but it said: Traceback (most recent call last): File charmm2gromacs-pvm.py, line 33, in module parFile = open(sys.argv[2], 'r') IndexError: list index out of range I open the script, it said: inparameters: command line parameters: 1charmm topology file 2corresponding charmm parameter file 3optfoldername, default cgenff.ff outfiles: 1foldername/atomtypes.atp 2foldername/forcefield.itp 3foldername/forcefield.doc 4foldername/aminoacids.rtp 5foldername/ffbonded.itp 6foldername/ffnonbonded.itp 7foldername/forcefield.r2b 8optfoldername/lipids.rtp(if '!lipid section' statement in CHARMM top file) 9optfoldername/cmap.itp(if genCMAP = True) It seems that the input file is a folder instead of a single file? I generate my ligand topology from the CGenFF website and I only get a .rst file THX -- 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] Fwd: Validation of topology ....
Dear Gromacs friends, I want to simulate a system containing the biotin. I get the topology from ATB. I want to validate these toplogy for my use . So please could some one told me the way how I can do it ?? I never had any such experience. Is these is any tutorial regarding to these. These is most difficult but needed things in MD. With best wishes and regards, Rama David. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to run charmm2gromacs-pvm.py correctly?
On 2012-11-27 17:58, Albert wrote: Hello: I am trying to convert the output from CGenFF website into Gromacs .itp format by command: python charmm2gromacs-pvm.py charmm.rst you need an extra file. IIRC the cgenff method gives you two files. but it said: Traceback (most recent call last): File charmm2gromacs-pvm.py, line 33, in module parFile = open(sys.argv[2], 'r') IndexError: list index out of range I open the script, it said: inparameters: command line parameters: 1charmm topology file 2corresponding charmm parameter file 3optfoldername, default cgenff.ff outfiles: 1foldername/atomtypes.atp 2foldername/forcefield.itp 3foldername/forcefield.doc 4foldername/aminoacids.rtp 5foldername/ffbonded.itp 6foldername/ffnonbonded.itp 7foldername/forcefield.r2b 8optfoldername/lipids.rtp(if '!lipid section' statement in CHARMM top file) 9optfoldername/cmap.itp(if genCMAP = True) It seems that the input file is a folder instead of a single file? I generate my ligand topology from the CGenFF website and I only get a .rst file THX -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@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/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] itp atomtypes section
Dear Tsjerk, Thanks for clarifying that for me. I appreciate it. Best regards, James On Tue, Nov 27, 2012 at 5:25 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi James, The 6 and 1 are the number of electrons the atomtype has, which is used for QM/MM stuff. Gromacs can tell whether or not it is given by checking the format of the line. If the 5th column is a letter, then the number isn't there, if the 6th column is a letter, it must be there. Hope it helps, Tsjerk On Tue, Nov 27, 2012 at 3:45 AM, James Cannon jamesresearch...@gmail.com wrote: Dear users, I apologise if this is a stupid question, however after a morning of searching I have not been able to find the answer. 1. I have a sample itp file and it contains a section like this: [ atomtypes ] CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01 HF HF 1 1.008000.1000 A3.5e-01 4.28529e-01 I can't work out what the column containing the 6 and 1 is for. Can anyone help? It's not documented anywhere that I can find. 2. I notice that there are many types of atomtypes fields. From the manual: [ atomtypes ] ;name mass charge ptype c6 c12 O 15.99940 0.000 A 0.22617E-02 0.74158E-06 OM 15.99940 0.000 A 0.22617E-02 0.74158E-06 This is clearly a different format to my sample above. Why does the format vary? I know the above format is not wrong because it runs succcessfully in a test-run. How does gromacs know which format to use correctly? I appreciate any help. Thank you. Best regards, James -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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] Gromacs 4.6 segmentation fault with mdrun
Dear GROMACS users: On Gromacs 4.6 segmentation fault with mdrun, I'd also met the same segmentation fault problem with gromacs-4.6. on my linux box with GTX-580. For my case, change the compilor solved this problem. Raf Ponsaerts wrote he used gcc 4.4.5 (Debian 4.4.5-8), Linux kernel 3.1.1 CMake 2.8.7 . These were same in the version when I first met the problem. After that, I'd tried Intel compilor instead of gcc-4.4.x, then the GPU jobs runs without the segmentation fault. I also tried gcc-4.6.x and it also runs without any faults (I'm using CentOS and its gcc version is currentry gcc-4.4.x. Then, I had to compile gcc-4.6.x from the source. gcc-4.7.x can't use with CUDA-4.2 since it only suppoorts up to gcc-4.6.x.). I suggest to try either intel compilor or gcc-4.6.x instead of gcc-4.4.x. Makoto Yoneya, Dr. AIST, Japan -- 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_bar and second law violations
On 11/27/12 11:43 AM, Sanku M wrote: Hi, I am trying to compute the free energy change using g_bar: I am using two-stage decoupling process as in Justin Lemkul's tutorial. But , I get following warning in all cases regarding violation of second law of thermodynamics. Can someone explain what is this error about and which lambda I should look for? Here is the output. You can't have negative entropy. Several of your simulation windows do, which indicates some severe problem, as the error suggests. -Justin Detailed results in kT (see help for explanation): lam_A lam_B DG +/- s_A +/- s_B +/- stdev +/- 0.000 0.100 -0.39 0.08 -0.64 0.06 -0.09 0.200.88 0.05 0.100 0.1500.08 0.040.07 0.030.09 0.050.43 0.01 0.150 0.2000.12 0.02 -0.11 0.030.36 0.060.54 0.02 0.200 0.3000.54 0.06 -0.05 0.071.25 0.151.24 0.03 0.300 0.3500.21 0.030.15 0.040.31 0.060.72 0.01 0.350 0.400 -0.01 0.020.11 0.03 -0.08 0.040.64 0.01 0.400 0.500 -0.37 0.030.22 0.02 -0.78 0.061.07 0.01 0.500 0.600 -0.58 0.010.17 0.04 -1.17 0.040.99 0.01 0.600 0.700 -0.74 0.030.16 0.02 -1.51 0.070.89 0.01 0.700 0.750 -0.37 0.01 -0.02 0.02 -0.69 0.030.47 0.01 0.750 0.800 -0.26 0.01 -0.07 0.01 -0.42 0.020.53 0.01 0.800 0.850 -0.19 0.010.03 0.01 -0.38 0.030.57 0.01 0.850 0.900 -0.24 0.020.06 0.01 -0.50 0.040.58 0.01 0.900 1.000 -0.47 0.07 -0.04 0.05 -0.12 0.341.13 0.06 WARNING: Some of these results violate the Second Law of Thermodynamics: This is can be the result of severe undersampling, or (more likely) there is something wrong with the simulations. Final results in kJ/mol: lambda 0.000 - 0.100, DG -0.97 +/- 0.19 lambda 0.100 - 0.150, DG 0.20 +/- 0.09 lambda 0.150 - 0.200, DG 0.30 +/- 0.05 lambda 0.200 - 0.300, DG 1.34 +/- 0.15 lambda 0.300 - 0.350, DG 0.52 +/- 0.07 lambda 0.350 - 0.400, DG -0.02 +/- 0.05 lambda 0.400 - 0.500, DG -0.92 +/- 0.08 lambda 0.500 - 0.600, DG -1.45 +/- 0.03 lambda 0.600 - 0.700, DG -1.86 +/- 0.08 lambda 0.700 - 0.750, DG -0.91 +/- 0.03 lambda 0.750 - 0.800, DG -0.64 +/- 0.03 lambda 0.800 - 0.850, DG -0.48 +/- 0.03 lambda 0.850 - 0.900, DG -0.61 +/- 0.04 lambda 0.900 - 1.000, DG -1.17 +/- 0.18 total 0.000 - 1.000, DG -6.68 +/- 0.30 -- 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] Re: About Temperature coupling and Energy Transfer....
Dear Justin Thanks for your answer. I know what you mean, but the problem is that this is not a possible physical (real) behaviour. If the temperature is not controlled as you said, the energy should continue growing not stop, but in these case after 50ps it reaches some kind of equilibrium and stabilize. So why this is happening? Can you give me with a Physical or and Algorithmic answer? Thanks John Michael -- View this message in context: http://gromacs.5086.n6.nabble.com/About-Temperature-coupling-and-Energy-Transfer-tp5003151p5003307.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
Re: [gmx-users] About the biotin parameter.....
Hi justin, Thank you for your suggestion. I read the ATB paper but the paper does not mention any thing related to the biotin. When I mail them, they replied .. To clarify the validation: There are different levels of validation criteria used in the ATB. The one which is available on the ATB web-site for a given molecule is the validation of the topology against the compatibility with the GROMOS force field. The output contains energies for bonded parameters. The validation described in the paper is the validation against the experimental hydration free energy of small organic molecules. Biotin was not a part of the validation dataset. What should I have to do..??? Please give me the suggestion. With best wishes and regards, Rama david -- 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
