Re: [gmx-users] Adding ions
The problem I was facing earlier: in the force field files (I am ussing ffG53a6) the ions are named NA+, CL-, for example, so with capital letters. Genion will add to the topology the ions named by default Na or Cl, unless you use the options -pname and/or -nname to name the ions. I do so and I have no mismatch of ionsname in different files. I hope this helps. Regards Andrea 2009/11/17 Arden Perkins > I am an undergraduate student and I am still learning to use GROMACS. When > I add my ions to the solution (using genion) by the procedure described in > the funnel web spider tutorial the .gro and .top files do not match. I tried > subtracting solvent molecules but they still dont match and I can't > continue. What am I doing wrong? > > Thanks! > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp error! why?
Dear gmx-users, I am try to simulate the protein-drug, and have used drg.itp from prodrg server2,5(beta). I have also got pro.top from pdb2gmx programs. But when I issue a grompp command for minimization,grompp gives a fatal error. The error is: Error 0 [file "unk.itp",line 4] Not enough parameters ….. Fatal error: Bonded/nonbonded atom type '1' not found! My pro.top file: #include “ffg43a1.itp” #include “unk.itp” [molecules] Protein1 UNK 1 SOL 109324 My drg.itp file: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CR1 1 UNK CBF 10.003 12.0110 2HC 1 UNK HBF 10.035 1.0080 ... [ bonds ] ; ai aj fuc0, c1, ... 1 2 20.109 1230.00.109 1230.0 ; CBF HBF 1 3 20.139 1080.00.139 1080.0 ; CBF CBG . [ pairs ] ; ai aj fuc0, c1, ... 1 6 1 ; CBF NBK 1 9 1 ; CBF CBI . [ angles ] ; ai aj ak fuc0, c1, ... 2 1 3 2120.0 505.0120.0 505.0 ; HBF CBF CBG 2 1 13 2120.0 505.0120.0 505.0 ; HBF CBF CBE [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 1 13 3 2 2 0.0 167.40.0 167.4 ; imp CBF CBE CBG HBF 3 1 5 4 2 0.0 167.40.0 167.4 ; imp CBG CBF CBH HBG Maybe someone knows what the problem might be?How can I deal with this problem? Thanks for your help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Tabulated non-bonded potential
Mark Abraham ha scritto: > ms wrote: >> Hi, >> >> I would like to understand a basic question about the usage of tabulated >> potential for non-bonded interaction. If I use an arbitrary function and >> I write a table for it, is the functional shape then applied to *all* my >> atoms, or can I specify which ones use the tabulated potential -and how? > > Use energygrp_table in the .mdp file. See manual section 7.3 *slap on my head* Thanks, I missed it. I was looking in the Chapters 4 and 5 and finding nothing I was confused. m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp error! why?
qing yang wrote: Dear gmx-users, I am try to simulate the protein-drug, and have used drg.itp from prodrg server2,5(beta). I have also got pro.top from pdb2gmx programs. But when PRODRG topologies are often unsatisfactory with respect to charges and charge groups assigned. Looking at the two relevant atom entries you've posted below, this is almost certainly the case. Please see the following: http://www.gromacs.org/Documentation/How-tos/Parameterization None of that is related specifically to your error, but I figured I should tell you before you waste your time simulating potentially unreliable parameters. I issue a grompp command for minimization,grompp gives a fatal error. The error is: Error 0 [file "unk.itp",line 4] Not enough parameters So you've pasted some of your topology below, but what exactly is on line 4? ….. Fatal error: Bonded/nonbonded atom type '1' not found! Is this a separate error? Please post all relevant output, otherwise it gets confusing. My pro.top file: This can't be right. You said pro.top came from pdb2gmx, so there should be substantially more in it. This is not to say that you need to post the entirety of your topology, but I doubt what you've shown is correct. This makes it hard to know if you've placed your #include statements appropriately, etc. #include “ffg43a1.itp” #include “unk.itp” [molecules] Protein1 UNK 1 SOL 109324 My drg.itp file: This snapshot does not provide any really useful information. Which of these lines, if any, is line 4, where grompp starts complaining? Shouldn't there be a [moleculetype] directive at the top of your .itp file, at the very least? Providing accurate information will get you to a solution a lot faster :) -Justin [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CR1 1 UNK CBF 10.003 12.0110 2HC 1 UNK HBF 10.035 1.0080 ... [ bonds ] ; ai aj fuc0, c1, ... 1 2 20.109 1230.00.109 1230.0 ; CBF HBF 1 3 20.139 1080.00.139 1080.0 ; CBF CBG . [ pairs ] ; ai aj fuc0, c1, ... 1 6 1 ; CBF NBK 1 9 1 ; CBF CBI . [ angles ] ; ai aj ak fuc0, c1, ... 2 1 3 2120.0 505.0120.0 505.0 ; HBF CBF CBG 2 1 13 2120.0 505.0120.0 505.0 ; HBF CBF CBE [ dihedrals ] ; ai aj ak al fuc0, c1, m, ... 1 13 3 2 2 0.0 167.40.0 167.4 ; imp CBF CBE CBG HBF 3 1 5 4 2 0.0 167.40.0 167.4 ; imp CBG CBF CBH HBG Maybe someone knows what the problem might be?How can I deal with this problem? Thanks for your help! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Decreasing MSD of ligand ?
Is the decrease occurs in the long times? Omer. On Tue, Nov 17, 2009 at 21:08, Chih-Ying Lin wrote: > > > > HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I > simulate the protein and ligand system and then calculate the MSD of the > ligand. Then, i drew the plot of the time evolution of the MSD. But the the > MSD decreases as time for some period. I see nothing about my codings. Would > you please tell me about any possible errors i made? Thank you Lin > > > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] vmd does not display the molecule
Hi I am trying to open a gromacs .gro file with VMD but VMD gives the following message upon opening and does not display the molecule : [ error reading box , unexpected end-of-file reached ] I checked number of atoms specified on the second line of the gro file and number of atoms really present in the file. It is ok. I also Checked that the box is correctly described at the last line of my file. please guied me -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] vmd does not display the molecule
leila karami wrote: Hi I am trying to open a gromacs .gro file with VMD but VMD gives the following message upon opening and does not display the molecule : [ error reading box , unexpected end-of-file reached ] I checked number of atoms specified on the second line of the gro file and number of atoms really present in the file. It is ok. I also Checked that the box is correctly described at the last line of my file. Well, if everything is right then you wouldn't have an error :) In any case, you haven't provided enough tangible evidence to diagnose the issue. If you can post the first few and last few lines of the .gro file (i.e. "head conf.gro" and "tail conf.gro"), maybe someone can spot the problem. Also, search the VMD mailing list, since this error has been posted there before. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] vmd does not display the molecule
dear justin I checked the VMD mailing list but that does not help me. first few lines of my gro file : Protein in water 23136 1GLY N1 1.655 4.898 3.866 -0.3222 -0.2420 0.1437 1GLY CA2 1.677 4.774 3.793 0.0134 -0.2201 0.2050 1GLYHA13 1.579 4.735 3.767 0.5541 -1.5676 0.1443 1GLYHA24 1.732 4.708 3.859 1.2946 2.0442 1.5391 1GLY C5 1.760 4.809 3.671 0.1350 -0.3085 0.2633 1GLY O6 1.732 4.904 3.598 0.1431 -0.4147 0.1209 2SER N7 1.867 4.733 3.644 0.3115 -0.0506 0.2274 2SER H8 1.898 4.660 3.706 -1.4080 -0.0311 1.1663 2SER CA9 1.924 4.738 3.511 -0.9271 0.2649 -0.3082 2SER HA 10 1.845 4.759 3.439 -0.6670 -0.9431 -0.9674 last few lines of my gro file : 7208Na Na23127 1.251 2.111 2.829 0.0512 -0.5390 0.2230 7209Na Na23128 0.220 2.894 0.285 -0.0656 0.2288 -0.0477 7210Na Na23129 2.803 0.503 5.080 0.0192 -0.1246 0.0370 7211Na Na23130 3.718 2.036 1.304 -0.4850 -0.3162 0.4396 7212Na Na23131 2.322 3.787 2.485 0.2661 0.1734 0.5773 7213Na Na23132 3.592 5.392 5.571 0.4515 0.6877 -0.3284 7214Na Na23133 4.708 2.478 0.651 -0.1105 0.1018 -0.4275 7215Na Na23134 4.612 4.964 0.340 0.2845 -0.3202 0.0326 7216Na Na23135 5.438 6.245 5.071 -0.0165 0.1414 -0.2011 7217Na Na23136 5.855 1.272 5.027 -0.3189 0.4687 -0.1455 6.21600 6.27700 6.26300 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp error! why?
You include unk.itp but show us drg.itp. Perhaps you're looking at or using the wrong file. /Erik qing yang skrev: Dear gmx-users, I am try to simulate the protein-drug, and have used drg.itp from prodrg server2,5(beta). I have also got pro.top from pdb2gmx programs. But when I issue a grompp command for minimization,grompp gives a fatal error. The error is: Error 0 [file "unk.itp",line 4] Not enough parameters ….. Fatal error: Bonded/nonbonded atom type '1' not found! My pro.top file: #include “ffg43a1.itp” #include “unk.itp” [molecules] Protein 1 UNK 1 SOL 109324 My drg.itp file: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CR1 1 UNK CBF 1 0.003 12.0110 2 HC 1 UNK HBF 1 0.035 1.0080 ... [ bonds ] ; ai aj fu c0, c1, ... 1 2 2 0.109 1230.0 0.109 1230.0 ; CBF HBF 1 3 2 0.139 1080.0 0.139 1080.0 ; CBF CBG . [ pairs ] ; ai aj fu c0, c1, ... 1 6 1 ; CBF NBK 1 9 1 ; CBF CBI . [ angles ] ; ai aj ak fu c0, c1, ... 2 1 3 2 120.0 505.0 120.0 505.0 ; HBF CBF CBG 2 1 13 2 120.0 505.0 120.0 505.0 ; HBF CBF CBE [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 1 13 3 2 2 0.0 167.4 0.0 167.4 ; imp CBF CBE CBG HBF 3 1 5 4 2 0.0 167.4 0.0 167.4 ; imp CBG CBF CBH HBG Maybe someone knows what the problem might be?How can I deal with this problem? Thanks for your help! -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] vmd does not display the molecule
leila karami wrote: dear justin I checked the VMD mailing list but that does not help me. first few lines of my gro file : Well, the structure of the .gro file appears intact. Somewhere along the way, VMD thinks it's hitting the end of the file. Have you manipulated or edited the file in any way? Opened it using some weird Windows software that saved some hidden characters or something? If so, you can run it through dos2unix to correct that. As an aside, what kind of model are you using? You have explicit HA atoms on the CA of GLY (OPLS? AMBER?), but no N-terminal protonation. That would seem to be a completely fictitious and unreasonable model for a standard N-terminal glycine. Not related to your problem, but I seem to be on a roll of free advice this morning :) -Justin Protein in water 23136 1GLY N1 1.655 4.898 3.866 -0.3222 -0.2420 0.1437 1GLY CA2 1.677 4.774 3.793 0.0134 -0.2201 0.2050 1GLYHA13 1.579 4.735 3.767 0.5541 -1.5676 0.1443 1GLYHA24 1.732 4.708 3.859 1.2946 2.0442 1.5391 1GLY C5 1.760 4.809 3.671 0.1350 -0.3085 0.2633 1GLY O6 1.732 4.904 3.598 0.1431 -0.4147 0.1209 2SER N7 1.867 4.733 3.644 0.3115 -0.0506 0.2274 2SER H8 1.898 4.660 3.706 -1.4080 -0.0311 1.1663 2SER CA9 1.924 4.738 3.511 -0.9271 0.2649 -0.3082 2SER HA 10 1.845 4.759 3.439 -0.6670 -0.9431 -0.9674 last few lines of my gro file : 7208Na Na23127 1.251 2.111 2.829 0.0512 -0.5390 0.2230 7209Na Na23128 0.220 2.894 0.285 -0.0656 0.2288 -0.0477 7210Na Na23129 2.803 0.503 5.080 0.0192 -0.1246 0.0370 7211Na Na23130 3.718 2.036 1.304 -0.4850 -0.3162 0.4396 7212Na Na23131 2.322 3.787 2.485 0.2661 0.1734 0.5773 7213Na Na23132 3.592 5.392 5.571 0.4515 0.6877 -0.3284 7214Na Na23133 4.708 2.478 0.651 -0.1105 0.1018 -0.4275 7215Na Na23134 4.612 4.964 0.340 0.2845 -0.3202 0.0326 7216Na Na23135 5.438 6.245 5.071 -0.0165 0.1414 -0.2011 7217Na Na23136 5.855 1.272 5.027 -0.3189 0.4687 -0.1455 6.21600 6.27700 6.26300 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp error! why?
2009/11/18 qing yang > Dear gmx-users, > > I am try to simulate the protein-drug, and have used drg.itp from prodrg > server2,5(beta). I have also got pro.top from pdb2gmx programs. But when I > issue a grompp command for minimization,grompp gives a fatal error. > > The error is: > > Error 0 [file "unk.itp",line 4] > > Not enough parameters > > ….. > > Fatal error: > > Bonded/nonbonded atom type '1' not found! > > My pro.top file: > >#include “ffg43a1.itp” > > Did you input this line with keyboard? Try #include "ffG43a1.itp" Terry #include “unk.itp” > >[molecules] > >Protein1 > >UNK 1 > >SOL 109324 > > My drg.itp file: > > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 CR1 1 UNK CBF 10.003 12.0110 > 2HC 1 UNK HBF 10.035 1.0080 >... > [ bonds ] > ; ai aj fuc0, c1, ... >1 2 20.109 1230.00.109 1230.0 ; CBF HBF >1 3 20.139 1080.00.139 1080.0 ; CBF CBG > . > [ pairs ] > ; ai aj fuc0, c1, ... >1 6 1 ; CBF NBK >1 9 1 ; CBF CBI >. > [ angles ] > ; ai aj ak fuc0, c1, ... >2 1 3 2120.0 505.0120.0 505.0 ; > HBF CBF CBG >2 1 13 2120.0 505.0120.0 505.0 ; > HBF CBF CBE > > [ dihedrals ] > ; ai aj ak al fuc0, c1, m, ... > 1 13 3 2 2 0.0 167.40.0 167.4 ; imp > CBF CBE CBG HBF > 3 1 5 4 2 0.0 167.40.0 167.4 ; imp > CBG CBF CBH HBG > Maybe someone knows what the problem might be?How can I deal with this > problem? > Thanks for your help! > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] vmd does not display the molecule
Hello, Did you try to just add a blank line at the end of the file? (after the box definition). Sometimes, that works for me. Otherwise, it could a problem of bad end-of-line character. That may happen if you have edited the file on Windows and try to visualize it on Linux. Nicolas leila karami a écrit : Hi I am trying to open a gromacs .gro file with VMD but VMD gives the following message upon opening and does not display the molecule : [ error reading box , unexpected end-of-file reached ] I checked number of atoms specified on the second line of the gro file and number of atoms really present in the file. It is ok. I also Checked that the box is correctly described at the last line of my file. please guied me <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] vmd does not display the molecule
dear justin I transfer gro files from linux to windows through SSH secure shell program. I added 10 Na ions by genion command but in gro file following case is appeared: 7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991 7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803 7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903 7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485 7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725 7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660 7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264 7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767 7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022 7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437 *7218ClCl231370.000 0.000 0.000 0. 0. 0. * 6.15463 6.21503 6.20117 I deleted line of7218ClCl231370.000 0.000 0.000 0. 0. 0. in top file following case is appeared: [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 SOL 7117 Na 10 Cl 0 I deleted last line. I am using amber03 force field in gromacs program to study interaction of pr-dna. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] vmd does not display the molecule
leila karami skrev: dear justin I transfer gro files from linux to windows through SSH secure shell program. I added 10 Na ions by genion command but in gro file following case is appeared: 7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991 7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803 7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903 7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485 7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725 7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660 7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264 7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767 7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022 7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437 *7218ClCl231370.000 0.000 0.000 0. 0. 0. * 6.15463 6.21503 6.20117 I deleted line of7218ClCl231370.000 0.000 0.000 0. 0. 0. in top file following case is appeared: [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 SOL 7117 Na 10 Cl 0 I deleted last line. I am using amber03 force field in gromacs program to study interaction of pr-dna. Not sure if it's related, but your topology doesn't match the gro-file. 0 Cl in top, but 1 in gro. /Erik -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] vmd does not display the molecule
Erik Marklund skrev: leila karami skrev: dear justin I transfer gro files from linux to windows through SSH secure shell program. I added 10 Na ions by genion command but in gro file following case is appeared: 7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991 7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803 7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903 7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485 7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725 7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660 7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264 7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767 7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022 7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437 *7218ClCl231370.000 0.000 0.000 0. 0. 0. * 6.15463 6.21503 6.20117 I deleted line of7218ClCl231370.000 0.000 0.000 0. 0. 0. in top file following case is appeared: [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 SOL 7117 Na 10 Cl 0 I deleted last line. I am using amber03 force field in gromacs program to study interaction of pr-dna. Not sure if it's related, but your topology doesn't match the gro-file. 0 Cl in top, but 1 in gro. /Erik Ignore my previous email. I missed that you deleted the Cl-related lines. So, did VMD display your system correctly before removing those lines? /Erik -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] vmd does not display the molecule
leila karami wrote: dear justin I transfer gro files from linux to windows through SSH secure shell program. I added 10 Na ions by genion command but in gro file following case is appeared: If an unrequested Cl is being added, then that is worth investigating. What was your *exact* genion command? Does the VMD error result in the edited file, or the one that has the additional Cl atom? 7208Na Na23127 1.533 2.176 2.687 0.1841 -0.1829 -0.2991 7209Na Na23128 0.179 2.821 0.336 -0.2683 -0.1820 0.5803 7210Na Na23129 2.288 0.458 4.819 -0.1171 0.7612 -0.4903 7211Na Na23130 3.640 1.815 1.138 -0.1083 -0.1591 0.0485 7212Na Na23131 2.183 3.845 1.964 -0.0409 -0.1492 0.6725 7213Na Na23132 3.356 5.216 5.834 -0.2686 0.1059 -0.1660 7214Na Na23133 4.304 2.510 0.809 -0.2994 0.3939 0.7264 7215Na Na23134 4.609 4.931 0.535 -0.2609 0.1315 -0.1767 7216Na Na23135 5.553 6.022 5.152 0.3516 -0.2021 0.2022 7217Na Na23136 5.865 1.114 5.034 0.0442 0.0272 0.3437 *7218ClCl231370.000 0.000 0.000 0. 0. 0. * 6.15463 6.21503 6.20117 I deleted line of7218ClCl231370.000 0.000 0.000 0. 0. 0. in top file following case is appeared: [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 SOL 7117 Na 10 Cl 0 I deleted last line. I am using amber03 force field in gromacs program to study interaction of pr-dna. Then I know that your model is wrong. You have no N-terminal protonation whatsoever! Think about biology before plowing ahead with computer programs that are only capable of doing what you tell them. Under AMBER, terminal residues require a prefix, i.e. NGLY (and CXXX for the C-terminal residues). This has been stated many times across this list, and is clearly in the ffamber documentation. Did you perhaps use the -missing flag with pdb2gmx when you got an error message? Perhaps this extra, unwanted, Cl atom is being added by genion because you have some bizarre fractional charge on your molecule? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Urea Topology
They are published in the paper by smith et al. (J. Phys. Chem. B 2004, 108, 1065-1071) and have also been posted previously on this mailing list (both of which can be found through a simple search). Please note that the parameters posted on the mailing list are not quite correct as they have they have the force constant for the impropers in kJ/mol/deg^2 not in kJ/mol/rad^2. Cheers Tom --On Tuesday, November 17, 2009 07:49:01 -0500 "Justin A. Lemkul" wrote: karan syal wrote: Dear All, I am looking for urea topology* (smith et al) *for gromos 96 force field. I tried searching through user contributions in gromacs site but couldnt find it. Is it possible for anyone who has already used it to mail me their toplogy file? If the parameters are published, you should probably contact the corresponding author to see if they will share. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pull code with defined negative relative displacements
Hi Berk, I have done the tests and you are entirely correct. I have one further question: If I simply want to pull to a relative displacement of -1.0 nm, is there any reason to prefer one of these methods, or are they just overlapping implementations of different methods that also have unique abilities given other settings? To summarize my tests, pull_geometry=direction can indeed pull to negative displacements and there is no bimodal behaviour. My misunderstanding derived from the fact that pull_geometry= direction pull_init1 = 1.0 pull_vec1= 0 0 1 gave the forces as I expected them, while pull_vec1= 0 0 -1 reports the negative of the force that I expected. Since the force as output is probably applied after multiplication by pull_vec1, it might be more intuitive to simply output the force after it is multiplied by pull_vec1 such that what is output is the actual applied force. But then again there are probably some good reasons why it is output the way that it is. I have included probability distribution plots for the sampling along z for the tests below at: http://i205.photobucket.com/albums/bb192/chrisneale_2007/X10.png (1.0 nm displacement test) http://i205.photobucket.com/albums/bb192/chrisneale_2007/X005.png (0.05 nm displacement test) http://i205.photobucket.com/albums/bb192/chrisneale_2007/X35.png (3.5 nm displacement test) Thank you for all of your assistance, Chris. # Summary for attempts to pull to -1.0: ### Pulls to -1 pull_geometry= position pull_init1 = 0 0 -1 pull_vec1= 0 0 0 pull_geometry= direction pull_init1 = -1.0 pull_vec1= 0 0 1 pull_geometry= direction pull_init1 = 1.0 pull_vec1= 0 0 -1 ### Pulls to +1 pull_geometry= direction pull_init1 = 1.0 pull_vec1= 0 0 1 # Detailed results: pull_geometry= position pull_init1 = 0 0 -1 pull_vec1= 0 0 0 $ tail coord.xvg 98.2000 5.03064 -0.96114 98.4000 5.02906 -0.968864 98.6000 5.02755 -1.0196 98.8000 5.02577 -0.971355 99. 5.02408 -0.948518 99.2000 5.02289 -0.973627 99.4000 5.0227 -0.977471 99.6000 5.02293 -0.965711 99.8000 5.0242 -1.01475 100.5.0251 -1.03216 $ tail force.xvg 98.2000 -19.4299 98.4000 -15.568 98.6000 9.8014 98.8000 -14.3227 99. -25.741 99.2000 -13.1865 99.4000 -11.2644 99.6000 -17.1443 99.8000 7.37747 100.16.0813 pull_geometry= direction pull_init1 = 1.0 pull_vec1= 0 0 1 $ tail coord.xvg 98.2000 5.06691 1.09005 98.4000 5.06773 1.04829 98.6000 5.06842 1.02481 98.8000 5.06934 1.02874 99. 5.07061 0.995157 99.2000 5.07164 0.990872 99.4000 5.07205 1.00651 99.6000 5.07256 1.02346 99.8000 5.07107 0.986439 100.5.06931 1.03009 $ tail force.xvg 98.2000 -45.0273 98.4000 -24.1432 98.6000 -12.4043 98.8000 -14.3716 99. 2.42147 99.2000 4.56404 99.4000 -3.25742 99.6000 -11.7324 99.8000 6.78027 100.-15.0443 ### where it does start at -1.0 $ grep -v '[#|@]' coord.xvg |head 0. 5.05992 -1.09968 0.2000 5.05948 -0.473992 0.4000 5.05982 0.43101 0.6000 5.06017 0.77986 0.8000 5.0609 0.78875 1. 5.06113 0.75552 1.2000 5.06151 0.750633 1.4000 5.06086 0.79958 1.6000 5.05976 0.821069 1.8000 5.05811 0.950296 ### pull_geometry= direction pull_init1 = -1.0 pull_vec1= 0 0 1 $ tail -n 30 coord.xvg|head -n 10 94.2000 5.04636 -1.00959 94.4000 5.04605 -1.09414 94.6000 5.04503 -1.09134 94.8000 5.0431 -1.10409 95. 5.04174 -1.05292 95.2000 5.04012 -1.03421 95.4000 5.03944 -1.05723 95.6000 5.03981 -1.00803 95.8000 5.04072 -1.01506 96. 5.04055 -0.980655 $ tail -n 30 force.xvg|head -n 10 94.2000 4.79288 94.4000 47.0722 94.6000 45.6695 94.8000 52.0426 95. 26.4623 95.2000 17.107 95.4000 28.6127 95.6000 4.0165 95.8000 7.52866 96. -9.67265 ### pull_geometry= direction pull_init1 = 1.0 pull_vec1= 0 0 -1 $ tail coord.xvg 98.2000 5.01781 -1.04195 98.4000 5.01766 -0.988034 98.6000 5.01789 -0.963644 98.8000 5.0185 -0.980899 99. 5.01958 -0.917222 99.2000 5.021 -1.00548 99.4000 5.02016 -0.970434 99.6000 5.01848 -1.01137 99.8000 5.01723 -0.950541 100.5.01743 -1.01916 $ tail force.xvg 98.2000 -20.9744 98.4000 5.98316 98.6000 18.1779 98.8000 9.55039 99. 41.3892 99.2000 -2.73847 99.4000 14.7832 99.6000 -5.68352 99.8000 24.7297 100.-9.58189 # # # # Summary for attempts to pull to -0.1: ### Pulls to -0.1 pull_geometry= position pull_init1 = 0 0 -0.1 pull_vec1
RE: [gmx-users] pull code with defined negative relative displacements
Hi, With only 1 pull dimension active (through pull_dims) all three geometries are equivalent. In 2 or 3D there are all different. With pull_geometry=direction the pull force is the force working along the direction vector. So in general you can't incorporate the direction (only sign in your case) into the force, unless you would print the whole vector. Berk > Date: Wed, 18 Nov 2009 12:12:49 -0500 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] pull code with defined negative relative displacements > > Hi Berk, > > I have done the tests and you are entirely correct. I have one further > question: If I simply want to pull to a relative displacement of -1.0 > nm, is there any reason to prefer one of these methods, or are they > just overlapping implementations of different methods that also have > unique abilities given other settings? > > To summarize my tests, pull_geometry=direction can indeed pull to negative > displacements and there is no bimodal behaviour. My misunderstanding > derived from the fact that > > pull_geometry= direction > pull_init1 = 1.0 > pull_vec1= 0 0 1 > > gave the forces as I expected them, while > > pull_vec1= 0 0 -1 > > reports the negative of the force that I expected. Since the force as > output is probably applied after multiplication by pull_vec1, it might > be more intuitive to simply output the force after it is multiplied by > pull_vec1 such that what is output is the actual applied force. But > then again there are probably some good reasons why it is output the > way that it is. > > I have included probability distribution plots for the sampling along z for > the tests below at: > http://i205.photobucket.com/albums/bb192/chrisneale_2007/X10.png (1.0 nm > displacement test) > http://i205.photobucket.com/albums/bb192/chrisneale_2007/X005.png (0.05 nm > displacement test) > http://i205.photobucket.com/albums/bb192/chrisneale_2007/X35.png (3.5 nm > displacement test) > > Thank you for all of your assistance, > Chris. > > # > Summary for attempts to pull to -1.0: > > ### Pulls to -1 > > pull_geometry= position > pull_init1 = 0 0 -1 > pull_vec1= 0 0 0 > > pull_geometry= direction > pull_init1 = -1.0 > pull_vec1= 0 0 1 > > pull_geometry= direction > pull_init1 = 1.0 > pull_vec1= 0 0 -1 > > ### Pulls to +1 > > pull_geometry= direction > pull_init1 = 1.0 > pull_vec1= 0 0 1 > > # > Detailed results: > > pull_geometry= position > pull_init1 = 0 0 -1 > pull_vec1= 0 0 0 > > $ tail coord.xvg > 98.2000 5.03064 -0.96114 > 98.4000 5.02906 -0.968864 > 98.6000 5.02755 -1.0196 > 98.8000 5.02577 -0.971355 > 99. 5.02408 -0.948518 > 99.2000 5.02289 -0.973627 > 99.4000 5.0227 -0.977471 > 99.6000 5.02293 -0.965711 > 99.8000 5.0242 -1.01475 > 100. 5.0251 -1.03216 > > $ tail force.xvg > 98.2000 -19.4299 > 98.4000 -15.568 > 98.6000 9.8014 > 98.8000 -14.3227 > 99. -25.741 > 99.2000 -13.1865 > 99.4000 -11.2644 > 99.6000 -17.1443 > 99.8000 7.37747 > 100. 16.0813 > > > > pull_geometry= direction > pull_init1 = 1.0 > pull_vec1= 0 0 1 > > $ tail coord.xvg > 98.2000 5.06691 1.09005 > 98.4000 5.06773 1.04829 > 98.6000 5.06842 1.02481 > 98.8000 5.06934 1.02874 > 99. 5.07061 0.995157 > 99.2000 5.07164 0.990872 > 99.4000 5.07205 1.00651 > 99.6000 5.07256 1.02346 > 99.8000 5.07107 0.986439 > 100. 5.06931 1.03009 > > $ tail force.xvg > 98.2000 -45.0273 > 98.4000 -24.1432 > 98.6000 -12.4043 > 98.8000 -14.3716 > 99. 2.42147 > 99.2000 4.56404 > 99.4000 -3.25742 > 99.6000 -11.7324 > 99.8000 6.78027 > 100. -15.0443 > > ### where it does start at -1.0 > > $ grep -v '[#|@]' coord.xvg |head > 0.5.05992 -1.09968 > 0.20005.05948 -0.473992 > 0.40005.05982 0.43101 > 0.60005.06017 0.77986 > 0.80005.0609 0.78875 > 1.5.06113 0.75552 > 1.20005.06151 0.750633 > 1.40005.06086 0.79958 > 1.60005.05976 0.821069 > 1.80005.05811 0.950296 > > ### > > pull_geometry= direction > pull_init1 = -1.0 > pull_vec1= 0 0 1 > > $ tail -n 30 coord.xvg|head -n 10 > 94.2000 5.04636 -1.00959 > 94.4000 5.04605 -1.09414 > 94.6000 5.04503 -1.09134 > 94.8000 5.0431 -1.10409 > 95. 5.04174 -1.05292 > 95.2000 5.
[gmx-users] constant_force pulling
Hi all, i tried out the constant_force pulling, to simulate a force clamp pulling experiment. But there are now some questions. But first describe the system and so on... The system consists of two molecules which can bind through hydrogen bonds with no water. Each molecule has one atom which will be consibered for the pulling. ZUG is that from the molecule that should be pulled and REF is the one from the other molecule (in umbrella pulling it would be the reference group). So the system looks the following REFhbonds-ZUG -> pulling in this direction. In the *.mdp file i had the following parameters: pull= constant_force pull_geometry = direction pull_dim= Y Y Y pull_ngroups= 1 pull_group1 = ZUG pull_k1 = -500 pull_vec1 = 1.631 0.196 0.279 where pull_vec1 is the vector from REF to ZUG. The manual states that for constant_force there is no reference group, so i took for pull_geometry direction, because it looks like that all the other options need a reference group. grompp complained that the pulling is in absolute coordinates and that this can lead to artefacts (i think when the molecule starts to rotate). In the end both molecule were pulled together through space, because REF wasn't fixed (so the molecule could move freely). Then i fixed the position of REF via position restraints and a freeze group (not both together, were two simulations). In both cases grompp didn't complain about the pulling in absolute coordinates. (I fixed the position of REF, because that's the same what the pullcode does in umbrella/position pulling with the reference group, the spring moves relative to the reference group so the reference group is fixed for the pulling). So now to my questions: 1) Would this (to fix the position of REF) be the right way to simulate a force clamp experiment? 2) If so, what would be better for fixing freeze group or position restraint? I tend to the former because then REF is fixed totally, in the later cases the two molecule would move a little bit, till the force from the pulling and restraint will be equilibrated and then i have nearly the same case as in the freeze group, but REF could fluctuate in space (how much depends on the strength of the restraints, but i think it would not be very much). 3) What to do with COM? Remove nothing, or only the translation or translation and rotation? One remark, i disabled the pbc, but i would be interesed what one should use best without and with pbc (in the later cases there could be also water present). Hope somebody has any ideas. 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] constant_force pulling
Hi, I think you mis-read the manual. With constant-force there is no reference position (since a linear potential has no reference point), but you can, and in your case should, use a reference group. Then you can also use the geometry distance. Berk > Date: Wed, 18 Nov 2009 19:08:43 +0100 > From: schl...@uni-mainz.de > To: gmx-users@gromacs.org > Subject: [gmx-users] constant_force pulling > > Hi all, > i tried out the constant_force pulling, to simulate a force clamp > pulling experiment. But there are now some questions. But first describe > the system and so on... > The system consists of two molecules which can bind through hydrogen > bonds with no water. Each molecule has one atom which will be consibered > for the pulling. ZUG is that from the molecule that should be pulled and > REF is the one from the other molecule (in umbrella pulling it would be > the reference group). So the system looks the following > REFhbonds-ZUG -> pulling in this direction. > > In the *.mdp file i had the following parameters: > pull= constant_force > pull_geometry = direction > pull_dim= Y Y Y > pull_ngroups= 1 > pull_group1 = ZUG > pull_k1 = -500 > pull_vec1 = 1.631 0.196 0.279 > > where pull_vec1 is the vector from REF to ZUG. > The manual states that for constant_force there is no reference group, > so i took for pull_geometry direction, because it looks like that all > the other options need a reference group. > > grompp complained that the pulling is in absolute coordinates and that > this can lead to artefacts (i think when the molecule starts to rotate). > In the end both molecule were pulled together through space, because REF > wasn't fixed (so the molecule could move freely). > > Then i fixed the position of REF via position restraints and a freeze > group (not both together, were two simulations). In both cases grompp > didn't complain about the pulling in absolute coordinates. (I fixed the > position of REF, because that's the same what the pullcode does in > umbrella/position pulling with the reference group, the spring moves > relative to the reference group so the reference group is fixed for the > pulling). > > So now to my questions: > > 1) Would this (to fix the position of REF) be the right way to simulate > a force clamp experiment? > > 2) If so, what would be better for fixing freeze group or position > restraint? I tend to the former because then REF is fixed totally, in > the later cases the two molecule would move a little bit, till the force > from the pulling and restraint will be equilibrated and then i have > nearly the same case as in the freeze group, but REF could fluctuate in > space (how much depends on the strength of the restraints, but i think > it would not be very much). > > 3) What to do with COM? Remove nothing, or only the translation or > translation and rotation? One remark, i disabled the pbc, but i would be > interesed what one should use best without and with pbc (in the later > cases there could be also water present). > > Hope somebody has any ideas. > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to construct fatty acid
Dear All: I'm new to Gromacs. I want to simulate water disolve in fatty acid (C-C-COOH) using a all atom model. I started up with constructing the pdb file of decanoic acid. Following the post by Justin http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also added the following [COOH] section into this file ; cooh [ COOH ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_267 0.52 2 O opls_268-0.5302 OTopls_269-0.44 2 HOopls_270 0.45 2 [ bonds ] C1-C2 C1H11 C1H12 C1C2 C2O C2OT OTHO [ impropers ] C1 OT C2 O improper_O_C_X_Y The following lines are also added to the .hdb file inaddition to those suggested in the aformentioned link COOH 2 2 6 H1 C1 C2 -C2 1 2 HO OT C2 C1 My pdb file is ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 COOH3 3.912 5.623 0.000 ATOM 6 C2 COOH3 5.368 6.124 0.000 ATOM 7 O COOH3 6.800 6.124 0.000 ATOM 8 OT COOH3 5.300 7.600 0.000 END I successfully constructed the .top file using pdb2gmx. However, when doing minimization, I found that the H attached to the O get too close to this O atom. I notice that there is no bond between these two atoms in the top file (a part of the top file is attached as follow): ; ; File 'acid.top' was generated ; By user: luotengf (482685) ; On host: dev-intel07 ; At date: Tue Nov 17 18:38:45 2009 ; ; This is your topology file ; "Drugs are Bad, mmokay" (South Park) ; ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_135 1 EthB C1 1 -0.18 12.011 ; qtot -0.18 2 opls_140 1 EthBH11 1 0.06 1.008 ; qtot -0.12 3 opls_140 1 EthBH12 1 0.06 1.008 ; qtot -0.06 4 opls_140 1 EthBH13 1 0.06 1.008 ; qtot 0 5 opls_136 1 EthB C2 2 -0.12 12.011 ; qtot -0.12 6 opls_140 1 EthBH21 2 0.06 1.008 ; qtot -0.06 7 opls_140 1 EthBH22 2 0.06 1.008 ; qtot 0 8 opls_136 2Eth C1 3 -0.12 12.011 ; qtot -0.12 9 opls_140 2EthH11 3 0.06 1.008 ; qtot -0.06 10 opls_140 2EthH12 3 0.06 1.008 ; qtot 0 11 opls_136 2Eth C2 4 -0.12 12.011 ; qtot -0.12 12 opls_140 2EthH21 4 0.06 1.008 ; qtot -0.06 13 opls_140 2EthH22 4 0.06 1.008 ; qtot 0 14 opls_136 3 COOH C1 5 -0.12 12.011 ; qtot -0.12 15 opls_140 3 COOHH11 5 0.06 1.008 ; qtot -0.06 16 opls_140 3 COOHH12 5 0.06 1.008 ; qtot 0 17 opls_267 3 COOH C2 6 0.52 12.011 ; qtot 0.52 18 opls_268 3 COOH O 6 -0.5315.9994 ; qtot -0.01 19 opls_269 3 COOH OT 6 -0.4415.9994 ; qtot -0.45 20 opls_270 3 COOH HO 6 0.45 1.008 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 5 7 1 5 8 1 8 9 1 810 1 811 1 1112 1 1113 1 1114 1 1415 1 1416 1 1417 1 1718 1 1719 1 Do you see what is wrong with my approach? I also know there is -ter which can replace the end with COOH, but how can I construct the termini to be replace at the first place? I tried to make myself as clear as possible and make the email short. I shall appreciate any help or suggestion. Sincerely, Tengfei -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to construct fatty acid
Tengfei Luo wrote: Dear All: I'm new to Gromacs. I want to simulate water disolve in fatty acid (C-C-COOH) using a all atom model. I started up with constructing the pdb file of decanoic acid. Following the post by Justin http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also added the following [COOH] section into this file ; cooh [ COOH ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_267 0.52 2 O opls_268-0.5302 OTopls_269-0.44 2 HOopls_270 0.45 2 [ bonds ] C1-C2 C1H11 C1H12 C1C2 C2O C2OT OTHO [ impropers ] C1 OT C2 O improper_O_C_X_Y The following lines are also added to the .hdb file inaddition to those suggested in the aformentioned link COOH 2 2 6 H1 C1 C2 -C2 1 2 HO OT C2 C1 My pdb file is ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 COOH3 3.912 5.623 0.000 ATOM 6 C2 COOH3 5.368 6.124 0.000 ATOM 7 O COOH3 6.800 6.124 0.000 ATOM 8 OT COOH3 5.300 7.600 0.000 END I successfully constructed the .top file using pdb2gmx. However, when doing minimization, I found that the H attached to the O get too close to this O atom. I notice that there is no bond between these two atoms in the top file (a part of the top file is attached as follow): Does the bond length change somehow? Or does the H get close to the carbonyl oxygen in the -COOH group? Are you doing the minimization in vacuo? If so, the strong (condensed-phase) charges that you have assigned may be inappropriate in the absence of solvent, which will screen electrostatic effects. The topology looks reasonable. Do you see what is wrong with my approach? I also know there is -ter which can replace the end with COOH, but how can I construct the termini to be replace at the first place? The -ter option does not function for non-protein compounds, as stated in the thread you cite. -Justin I tried to make myself as clear as possible and make the email short. I shall appreciate any help or suggestion. Sincerely, Tengfei -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to construct fatty acid
Justin: Thank you for your help! Yes, the OH bond length changed before and after minimization. and yes, the H get close to the carbonyl O in the COOH group. I did the minimization with solvent. I appreciate any further suggestion! Tengfei - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, November 18, 2009 2:21 PM Subject: Re: [gmx-users] how to construct fatty acid Tengfei Luo wrote: Dear All: I'm new to Gromacs. I want to simulate water disolve in fatty acid (C-C-COOH) using a all atom model. I started up with constructing the pdb file of decanoic acid. Following the post by Justin http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also added the following [COOH] section into this file ; cooh [ COOH ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_267 0.52 2 O opls_268-0.5302 OTopls_269-0.44 2 HOopls_270 0.45 2 [ bonds ] C1-C2 C1H11 C1H12 C1C2 C2O C2OT OTHO [ impropers ] C1 OT C2 O improper_O_C_X_Y The following lines are also added to the .hdb file inaddition to those suggested in the aformentioned link COOH 2 2 6 H1 C1 C2 -C2 1 2 HO OT C2 C1 My pdb file is ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 COOH3 3.912 5.623 0.000 ATOM 6 C2 COOH3 5.368 6.124 0.000 ATOM 7 O COOH3 6.800 6.124 0.000 ATOM 8 OT COOH3 5.300 7.600 0.000 END I successfully constructed the .top file using pdb2gmx. However, when doing minimization, I found that the H attached to the O get too close to this O atom. I notice that there is no bond between these two atoms in the top file (a part of the top file is attached as follow): Does the bond length change somehow? Or does the H get close to the carbonyl oxygen in the -COOH group? Are you doing the minimization in vacuo? If so, the strong (condensed-phase) charges that you have assigned may be inappropriate in the absence of solvent, which will screen electrostatic effects. The topology looks reasonable. Do you see what is wrong with my approach? I also know there is -ter which can replace the end with COOH, but how can I construct the termini to be replace at the first place? The -ter option does not function for non-protein compounds, as stated in the thread you cite. -Justin I tried to make myself as clear as possible and make the email short. I shall appreciate any help or suggestion. Sincerely, Tengfei -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to construct fatty acid
Tengfei Luo wrote: Justin: Thank you for your help! Yes, the OH bond length changed before and after minimization. and yes, the H get close to the carbonyl O in the COOH group. I did the minimization with solvent. I appreciate any further suggestion! Can you post your .mdp file? I have never seen any instability in OPLS -COOH groups like you've described. -Justin Tengfei - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, November 18, 2009 2:21 PM Subject: Re: [gmx-users] how to construct fatty acid Tengfei Luo wrote: Dear All: I'm new to Gromacs. I want to simulate water disolve in fatty acid (C-C-COOH) using a all atom model. I started up with constructing the pdb file of decanoic acid. Following the post by Justin http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also added the following [COOH] section into this file ; cooh [ COOH ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_267 0.52 2 O opls_268-0.5302 OTopls_269-0.44 2 HOopls_270 0.45 2 [ bonds ] C1-C2 C1H11 C1H12 C1C2 C2O C2OT OTHO [ impropers ] C1 OT C2 O improper_O_C_X_Y The following lines are also added to the .hdb file inaddition to those suggested in the aformentioned link COOH 2 2 6 H1 C1 C2 -C2 1 2 HO OT C2 C1 My pdb file is ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 COOH3 3.912 5.623 0.000 ATOM 6 C2 COOH3 5.368 6.124 0.000 ATOM 7 O COOH3 6.800 6.124 0.000 ATOM 8 OT COOH3 5.300 7.600 0.000 END I successfully constructed the .top file using pdb2gmx. However, when doing minimization, I found that the H attached to the O get too close to this O atom. I notice that there is no bond between these two atoms in the top file (a part of the top file is attached as follow): Does the bond length change somehow? Or does the H get close to the carbonyl oxygen in the -COOH group? Are you doing the minimization in vacuo? If so, the strong (condensed-phase) charges that you have assigned may be inappropriate in the absence of solvent, which will screen electrostatic effects. The topology looks reasonable. Do you see what is wrong with my approach? I also know there is -ter which can replace the end with COOH, but how can I construct the termini to be replace at the first place? The -ter option does not function for non-protein compounds, as stated in the thread you cite. -Justin I tried to make myself as clear as possible and make the email short. I shall appreciate any help or suggestion. Sincerely, Tengfei -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to construct fatty acid
Here it is: title = acid cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE ; use flexible water model constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 400 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Thank you again! Tengfei - Original Message - From: "Justin A. Lemkul" To: "Gromacs Users' List" Sent: Wednesday, November 18, 2009 2:34 PM Subject: Re: [gmx-users] how to construct fatty acid Tengfei Luo wrote: Justin: Thank you for your help! Yes, the OH bond length changed before and after minimization. and yes, the H get close to the carbonyl O in the COOH group. I did the minimization with solvent. I appreciate any further suggestion! Can you post your .mdp file? I have never seen any instability in OPLS -COOH groups like you've described. -Justin Tengfei - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, November 18, 2009 2:21 PM Subject: Re: [gmx-users] how to construct fatty acid Tengfei Luo wrote: Dear All: I'm new to Gromacs. I want to simulate water disolve in fatty acid (C-C-COOH) using a all atom model. I started up with constructing the pdb file of decanoic acid. Following the post by Justin http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also added the following [COOH] section into this file ; cooh [ COOH ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_267 0.52 2 O opls_268-0.5302 OTopls_269-0.44 2 HOopls_270 0.45 2 [ bonds ] C1-C2 C1H11 C1H12 C1C2 C2O C2OT OTHO [ impropers ] C1 OT C2 O improper_O_C_X_Y The following lines are also added to the .hdb file inaddition to those suggested in the aformentioned link COOH 2 2 6 H1 C1 C2 -C2 1 2 HO OT C2 C1 My pdb file is ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 COOH3 3.912 5.623 0.000 ATOM 6 C2 COOH3 5.368 6.124 0.000 ATOM 7 O COOH3 6.800 6.124 0.000 ATOM 8 OT COOH3 5.300 7.600 0.000 END I successfully constructed the .top file using pdb2gmx. However, when doing minimization, I found that the H attached to the O get too close to this O atom. I notice that there is no bond between these two atoms in the top file (a part of the top file is attached as follow): Does the bond length change somehow? Or does the H get close to the carbonyl oxygen in the -COOH group? Are you doing the minimization in vacuo? If so, the strong (condensed-phase) charges that you have assigned may be inappropriate in the absence of solvent, which will screen electrostatic effects. The topology looks reasonable. Do you see what is wrong with my approach? I also know there is -ter which can replace the end with COOH, but how can I construct the termini to be replace at the first place? The -ter option does not function for non-protein compounds, as stated in the thread you cite. -Justin I tried to make myself as clear as possible and make the email short. I shall appreciate any help or suggestion. Sincerely, Tengfei -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or s
Re: [gmx-users] how to construct fatty acid
When I run grompp using all your files, I get a series of errors: ERROR 1 [file topol.top, line 60]: No default Bond types ERROR 2 [file topol.top, line 144]: No default Angle types ERROR 3 [file topol.top, line 190]: No default Ryckaert-Bell. types ERROR 4 [file topol.top, line 191]: No default Ryckaert-Bell. types How did you deal with these? The first refers to the OT-HO bond, for which there is no known bond type, and the rest are a result of the same problematic atom types. I think you have the carboxylate oxygen types wrong. The carbonyl O should be opls_269, and the acid O (in the -OH functional group) should be opls_268. These atom types are taken from the ASPH .rtp entry. If you switch them, the errors go away and the structure produced seems reasonable. -Justin Tengfei Luo wrote: Here it is: title = acid cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE ; use flexible water model constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 400 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Thank you again! Tengfei - Original Message - From: "Justin A. Lemkul" To: "Gromacs Users' List" Sent: Wednesday, November 18, 2009 2:34 PM Subject: Re: [gmx-users] how to construct fatty acid Tengfei Luo wrote: Justin: Thank you for your help! Yes, the OH bond length changed before and after minimization. and yes, the H get close to the carbonyl O in the COOH group. I did the minimization with solvent. I appreciate any further suggestion! Can you post your .mdp file? I have never seen any instability in OPLS -COOH groups like you've described. -Justin Tengfei - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, November 18, 2009 2:21 PM Subject: Re: [gmx-users] how to construct fatty acid Tengfei Luo wrote: Dear All: I'm new to Gromacs. I want to simulate water disolve in fatty acid (C-C-COOH) using a all atom model. I started up with constructing the pdb file of decanoic acid. Following the post by Justin http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also added the following [COOH] section into this file ; cooh [ COOH ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_267 0.52 2 O opls_268-0.5302 OTopls_269-0.44 2 HOopls_270 0.45 2 [ bonds ] C1-C2 C1H11 C1H12 C1C2 C2O C2OT OTHO [ impropers ] C1 OT C2 O improper_O_C_X_Y The following lines are also added to the .hdb file inaddition to those suggested in the aformentioned link COOH 2 2 6 H1 C1 C2 -C2 1 2 HO OT C2 C1 My pdb file is ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 COOH3 3.912 5.623 0.000 ATOM 6 C2 COOH3 5.368 6.124 0.000 ATOM 7 O COOH3 6.800 6.124 0.000 ATOM 8 OT COOH3 5.300 7.600 0.000 END I successfully constructed the .top file using pdb2gmx. However, when doing minimization, I found that the H attached to the O get too close to this O atom. I notice that there is no bond between these two atoms in the top file (a part of the top file is attached as follow): Does the bond length change somehow? Or does the H get close to the carbonyl oxygen in the -COOH group? Are you doing the minimization in vacuo? If so, the strong (condensed-phase) charges that you have assigned may be inappropriate in the absence of solvent, which will screen electrostatic effects. The topology looks reasonable. Do you see what is wrong with my approach? I also know there is -ter which can replace the end with COOH, but how can I construct the termini to be replace at the first place? The -ter option does not function for non-protein compounds, as stated in the thread you cite. -Justin I tried to make myself as clear as possible and make the email short. I shall appreciate any help or suggestion. Sincerely, Tengfei -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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
Re: [gmx-users] how to construct fatty acid
Justin: Thank you very much! It worked and everything seems reasonable now. Regards, Tengfei - Original Message - From: "Justin A. Lemkul" To: "Gromacs Users' List" Sent: Wednesday, November 18, 2009 2:47 PM Subject: Re: [gmx-users] how to construct fatty acid When I run grompp using all your files, I get a series of errors: ERROR 1 [file topol.top, line 60]: No default Bond types ERROR 2 [file topol.top, line 144]: No default Angle types ERROR 3 [file topol.top, line 190]: No default Ryckaert-Bell. types ERROR 4 [file topol.top, line 191]: No default Ryckaert-Bell. types How did you deal with these? The first refers to the OT-HO bond, for which there is no known bond type, and the rest are a result of the same problematic atom types. I think you have the carboxylate oxygen types wrong. The carbonyl O should be opls_269, and the acid O (in the -OH functional group) should be opls_268. These atom types are taken from the ASPH .rtp entry. If you switch them, the errors go away and the structure produced seems reasonable. -Justin Tengfei Luo wrote: Here it is: title = acid cpp = /usr/bin/cpp ; the c pre-processor define = -DFLEXIBLE ; use flexible water model constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 400 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 Thank you again! Tengfei - Original Message - From: "Justin A. Lemkul" To: "Gromacs Users' List" Sent: Wednesday, November 18, 2009 2:34 PM Subject: Re: [gmx-users] how to construct fatty acid Tengfei Luo wrote: Justin: Thank you for your help! Yes, the OH bond length changed before and after minimization. and yes, the H get close to the carbonyl O in the COOH group. I did the minimization with solvent. I appreciate any further suggestion! Can you post your .mdp file? I have never seen any instability in OPLS -COOH groups like you've described. -Justin Tengfei - Original Message - From: "Justin A. Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, November 18, 2009 2:21 PM Subject: Re: [gmx-users] how to construct fatty acid Tengfei Luo wrote: Dear All: I'm new to Gromacs. I want to simulate water disolve in fatty acid (C-C-COOH) using a all atom model. I started up with constructing the pdb file of decanoic acid. Following the post by Justin http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html I added the [Eth] and [EthB] part into the ffoplsaa.rtp file. I also added the following [COOH] section into this file ; cooh [ COOH ] [ atoms ] C1opls_136-0.1201 H11 opls_140 0.0601 H12 opls_140 0.0601 C2opls_267 0.52 2 O opls_268-0.5302 OTopls_269-0.44 2 HOopls_270 0.45 2 [ bonds ] C1-C2 C1H11 C1H12 C1C2 C2O C2OT OTHO [ impropers ] C1 OT C2 O improper_O_C_X_Y The following lines are also added to the .hdb file inaddition to those suggested in the aformentioned link COOH 2 2 6 H1 C1 C2 -C2 1 2 HO OT C2 C1 My pdb file is ATOM 1 C1 EthB1 1.000 1.540 0.000 ATOM 2 C2 EthB1 2.456 2.041 0.000 ATOM 3 C1 Eth 2 2.456 3.581 0.000 ATOM 4 C2 Eth 2 3.912 4.083 0.000 ATOM 5 C1 COOH3 3.912 5.623 0.000 ATOM 6 C2 COOH3 5.368 6.124 0.000 ATOM 7 O COOH3 6.800 6.124 0.000 ATOM 8 OT COOH3 5.300 7.600 0.000 END I successfully constructed the .top file using pdb2gmx. However, when doing minimization, I found that the H attached to the O get too close to this O atom. I notice that there is no bond between these two atoms in the top file (a part of the top file is attached as follow): Does the bond length change somehow? Or does the H get close to the carbonyl oxygen in the -COOH group? Are you doing the minimization in vacuo? If so, the strong (condensed-phase) charges that you have assigned may be inappropriate in the absence of solvent, which will screen electrostatic effects. The topology looks reasonable. Do you see what is wrong with my approach? I also know there is -ter which can replace the end with COOH, but how can I construct the termini to be replace at the first place? The -ter option does not function for non-protein compounds, as stated in the thread you cite. -Justin I tried to make myself as clear as possible and make the email short. I shall appreciate any help or suggestion. Sincerely, Tengfei -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar De
SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote:
> Dear gmx-users,
>
>
>
> I have done simulations of one small molecule that diffuses into a DMPC
> membrane. This small molecule contains an alcohol group and is therefore
> capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol
> region).
>
> I have read the manual (section 8.12 and g_hbond -h), searched the mailing
> list and google but I have not been able to find a more thorough description
> of the output possibilities than in the manual.
>
> I have tried three different approaches:
>
> 1. The -OH group of the small molecule and the glycerol oxygens
>
> 2. The -OH group of the small molecule and the phosphate oxygens
>
> 3. The small molecule and DMPC (no subgroups)
>
> No. 1 gives 38 hbond, no. 2 gives 15 hbonds and no. 3 gives 53 hbonds. So 1 +
> 2 = 3, which is fine.
>
I'm assuming this is just some theoretical limit that you have established, and
not something that has actually been calculated, correct?
This is from the output of the program, you have explained it below :-)
>
>
> Below is the output from no. 1: (gromacs 4.0.4)
>
> Specify 2 groups to analyze:
>
> Selected 0: 'O11_&_PALC_H12_&_PALC'
>
> Selected 1: 'O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC'
>
> Checking for overlap in atoms between O11_&_PALC_H12_&_PALC and
> O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC
>
> Calculating hydrogen bonds between O11_&_PALC_H12_&_PALC (2 atoms) and
> O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC (384 atoms)
>
> Found 1 donors and 385 acceptors
>
> Making hbmap structure...done.
>
>
>
> Will do grid-seach on 15x15x24 grid, rcut=0.35
>
> Found 15 different hydrogen bonds in trajectory
>
> Found 23 different atom-pairs within hydrogen bonding distance
>
> Merging hbonds with Acceptor and Donor swapped
>
> - Reduced number of hbonds from 15 to 15
>
> - Reduced number of distances from 23 to 23
>
> Average number of hbonds per timeframe 0.083 out of 192.5 possible
>
>
>
> What does these "15 different hydrogen bond in trajectory" mean? I don't
> understand this. I also don't understand "Average number of hbonds per
That means quite literally what it says: there are 15 distinct hydrogen bonds
that form at some point in your trajectory. They are listed in hbond.ndx
(output of -hbn) and mapped in hbmap.xpm (from -hbm). You should find that
there are 15 :)
Yes, I see this. Do you by the way know why this .ndx files under the title [
donors_hydrogens_DMPC ] lists a lot of non-heteroatoms (carbon atoms)?
> timeframe 0.083 out of 192.5 possible" - 192.5 possible hbonds?? Can anyone
> shed some light on this?
You have 385 H-bond acceptors (see the output above). It appears that g_hbond
makes a simple assumption that if half of these were occupied (with the other
half of the group serving as a donor, which may or may not ever have any
physical significance), then the maximum number of H-bonds would be 385/2 =
192.5.
The average printed is simply the average number of H-bonds that are present
between your two groups at any given time. If your small molecule has only one
-OH group that you're considering, the maximum number of H-bonds per timeframe
is 1.
Ok.
>
>
>
> Another question relates to the lifetime of the hbond calculated when the
> "-life" flag is given. The produced .xvg file contain three columns: time,
> p(t), and t p(t). What is p(t) and t p(t)? And how can I find the lifetime?
>
>
The explanation is probably in one of the "Please read and cite the following
reference" messages that g_hbond spits out. Looks like some sort of probability
function. You should also be cautioned by this warning from using the -life
option:
"Note that the lifetime obtained in this manner is close to useless
Use the -ac option instead and check the Forward lifetime"
When I use the -ac option I get this output:
...
ACF 53/53
Normalization for c(t) = 1.19876 for gh(t) = 9.96115e-05
WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) > 0.001
Tail value (average C(t) over second half of acf): 0.0155651 +/- 0.014574
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 5.76828e-05
Q = 0
--
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.001682.571 20.705 5.76828e-05
Backward0.013 75.432 15.245
One-way 0.001 1001.338 21.655
Integral0.000 3419.839 24.700
Relaxation 0.001 1216.745 22.138
100%
...
When looking at the produced .xvg file I see these three data sets as a
function of time:
@ s0 legend "Ac\sfin sys\v{}\z{}(t)"
@ s1 legend "Ac(t)"
@ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
@ s3 legend "-dAc\sfs\v{}\z{}/dt"
In neither the output nor the .xvg file I see any mention of 'Forward
lifetime'. Perhabs this is because of the warning 'Correlation function is
probably not long enough because the standard deviation in the ta
[gmx-users] Decreasing MSD of ligand ?
Hi The MSD decrease occurs in the long times. The ligand has bounded to a protein. How can the decrease happen? Thank you Lin Chih-Ying Lin wrote: > > > > HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I > simulate the protein and ligand system and then calculate the MSD of the > ligand. Then, i drew the plot of the time evolution of the MSD. But the > the MSD decreases as time for some period. I see nothing about my > codings. Would you please tell me about any possible errors i made? MSD can decrease due to insufficient sampling (time of the simulation, number of frames analyzed, etc). Depending on what you define as "some period" (during the initial part of the simulation? the middle? the end?) the behavior may or may not be normal, but from the few details you provide, there's no way to know. What do you hope to see in this analysis? Will a ligand bound to a protein really diffuse that much anyway? -Justin > Thank you Lin > > > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote:
Yes, I see this. Do you by the way know why this .ndx files under the title [ donors_hydrogens_DMPC ] lists a lot of non-heteroatoms (carbon atoms)?
No clue. Probably the code identifies the functional group to which the donor
belongs. The more pertinent directive is the [ hbonds... ] one, which contains
the indices of the atoms actually participating in hydrogen bonding.
When I use the -ac option I get this output:
...
ACF 53/53
Normalization for c(t) = 1.19876 for gh(t) = 9.96115e-05
WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) > 0.001
Tail value (average C(t) over second half of acf): 0.0155651 +/- 0.014574
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 5.76828e-05
Q = 0
--
Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
Forward 0.001682.571 20.705 5.76828e-05
Backward0.013 75.432 15.245
One-way 0.001 1001.338 21.655
Integral0.000 3419.839 24.700
Relaxation 0.001 1216.745 22.138
100%
...
When looking at the produced .xvg file I see these three data sets as a function of time:
@ s0 legend "Ac\sfin sys\v{}\z{}(t)"
@ s1 legend "Ac(t)"
@ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
@ s3 legend "-dAc\sfs\v{}\z{}/dt"
In neither the output nor the .xvg file I see any mention of 'Forward lifetime'. Perhabs this is because of the warning 'Correlation function is probably not long enough because the standard deviation in the tail of C(t) > 0.001' which I sadly don't understand. Is this a matter of actual length of the .xtc file? I use the last 120 ns of a 220 ns simulation. Any suggestions?
Please see the following output line:
Forward 0.001682.571 20.705 5.76828e-05
The note about the correlation function would imply that the correlation
function itself has not converged until its value is < 0.001. This is usually a
result of insufficient data, either the length of the simulation, or number of
frames analyzed (based on the spacing of the frames).
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Decreasing MSD of ligand ?
Chih-Ying Lin wrote: Hi The MSD decrease occurs in the long times. The ligand has bounded to a protein. How can the decrease happen? Probably because the ligand, being bound to the protein, has its motion restricted by its interaction with the protein. I don't see the purpose of measuring the MSD of a bound compound, since it probably shouldn't change much, anyway, if the ligand remains in the active site. MSD is much more useful for measuring the movement of more freely-diffusible entities (solvents, lipids, etc). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote:
>
> Yes, I see this. Do you by the way know why this .ndx files under the title [
> donors_hydrogens_DMPC ] lists a lot of non-heteroatoms (carbon atoms)?
>
No clue. Probably the code identifies the functional group to which the donor
belongs. The more pertinent directive is the [ hbonds... ] one, which contains
the indices of the atoms actually participating in hydrogen bonding.
> When I use the -ac option I get this output:
> ...
> ACF 53/53
> Normalization for c(t) = 1.19876 for gh(t) = 9.96115e-05
> WARNING: Correlation function is probably not long enough
> because the standard deviation in the tail of C(t) > 0.001
> Tail value (average C(t) over second half of acf): 0.0155651 +/- 0.014574
> Hydrogen bond thermodynamics at T = 298.15 K
> Fitting parameters chi^2 = 5.76828e-05
> Q = 0
> --
> Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
> Forward 0.001682.571 20.705 5.76828e-05
> Backward0.013 75.432 15.245
> One-way 0.001 1001.338 21.655
> Integral0.000 3419.839 24.700
> Relaxation 0.001 1216.745 22.138
> 100%
> ...
>
> When looking at the produced .xvg file I see these three data sets as a
> function of time:
> @ s0 legend "Ac\sfin sys\v{}\z{}(t)"
> @ s1 legend "Ac(t)"
> @ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
> @ s3 legend "-dAc\sfs\v{}\z{}/dt"
>
>
> In neither the output nor the .xvg file I see any mention of 'Forward
> lifetime'. Perhabs this is because of the warning 'Correlation function is
> probably not long enough because the standard deviation in the tail of C(t) >
> 0.001' which I sadly don't understand. Is this a matter of actual length of
> the .xtc file? I use the last 120 ns of a 220 ns simulation. Any suggestions?
>
Please see the following output line:
Forward 0.001682.571 20.705 5.76828e-05
ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per
hbond is 628.571 ps?
The note about the correlation function would imply that the correlation
function itself has not converged until its value is < 0.001. This is usually a
result of insufficient data, either the length of the simulation, or number of
frames analyzed (based on the spacing of the frames).
Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps)
is not long enough. Perhabs I should try the original .trr file... The .xtc
file I'm using only contains DMPC and the small molecule, no solvent - I can't
see this would make a difference in this case, am I right?
Thank you,
Sarah
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Re: SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote: ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per hbond is 628.571 ps? Yes, per the calculation. For a bit more about the analysis, see the "Please read and cite" notices, as well as this thread: http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html The note about the correlation function would imply that the correlation function itself has not converged until its value is < 0.001. This is usually a result of insufficient data, either the length of the simulation, or number of frames analyzed (based on the spacing of the frames). Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps) is not long enough. Perhabs I should try the original .trr file... The .xtc file I'm using only contains DMPC and the small molecule, no solvent - I can't see this would make a difference in this case, am I right? The correlation will depend on how much the interactions are changing over the period you analyzed. If you are analyzing a small molecule and DMPC, water should not matter. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
SV: SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote: > ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per > hbond is 628.571 ps? > Yes, per the calculation. For a bit more about the analysis, see the "Please read and cite" notices, as well as this thread: http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html > The note about the correlation function would imply that the correlation > function itself has not converged until its value is < 0.001. This is > usually a > result of insufficient data, either the length of the simulation, or number of > frames analyzed (based on the spacing of the frames). > > Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps) > is not long enough. Perhabs I should try the original .trr file... The .xtc > file I'm using only contains DMPC and the small molecule, no solvent - I > can't see this would make a difference in this case, am I right? > The correlation will depend on how much the interactions are changing over the period you analyzed. If you are analyzing a small molecule and DMPC, water should not matter. I have now tried with the full length (220 ns) .trr file and the -ac output still prints a warning: ACF 106/106 Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) > 0.001 Tail value (average C(t) over second half of acf): 0.000172327 +/- 0.00277407 In your opinion, does this mean that I cannot trust the value of the lifetime, since the correlation function is not converging? Thank you! I have conducted the analysis on the -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: SV: SV: SV: [gmx-users] Hydrogen bonding
Sarah Witzke wrote: Sarah Witzke wrote: ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per hbond is 628.571 ps? Yes, per the calculation. For a bit more about the analysis, see the "Please read and cite" notices, as well as this thread: http://lists.gromacs.org/pipermail/gmx-users/2009-February/039955.html The note about the correlation function would imply that the correlation function itself has not converged until its value is < 0.001. This is usually a result of insufficient data, either the length of the simulation, or number of frames analyzed (based on the spacing of the frames). Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps) is not long enough. Perhabs I should try the original .trr file... The .xtc file I'm using only contains DMPC and the small molecule, no solvent - I can't see this would make a difference in this case, am I right? The correlation will depend on how much the interactions are changing over the period you analyzed. If you are analyzing a small molecule and DMPC, water should not matter. I have now tried with the full length (220 ns) .trr file and the -ac output still prints a warning: ACF 106/106 Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05 WARNING: Correlation function is probably not long enough because the standard deviation in the tail of C(t) > 0.001 Tail value (average C(t) over second half of acf): 0.000172327 +/- 0.00277407 In your opinion, does this mean that I cannot trust the value of the lifetime, since the correlation function is not converging? I'm not entirely sure. Please see the posts from David in the thread I referenced before about some potential issues with the ACF in the g_hbond calculation. I assume you are using version 4.0.x? -Justin Thank you! I have conducted the analysis on the -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem with box-type after the extension of simulation
Dear All, I started a protein simulation for 100ps with octahedron box. After completion of that run I visualized the protein at the centre of the octahedron box by using trjconv. Then I have extended the simulation for another 500 ps by using tpbconv. But now it is showing as cubic box when I see the result after using trajconv (additionally some part of the protein is out of the box). I do not have any clue how the box type has been changed or where could I go wrong. Please comment. Thank you, Cheers, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with box-type after the extension of simulation
On Wed, Nov 18, 2009 at 9:29 PM, sukesh chandra gain wrote: > Dear All, > I started a protein simulation for 100ps with octahedron box. After > completion of that run I visualized the protein at the centre of the > octahedron box by using trjconv. > Then I have extended the simulation for another 500 ps by using tpbconv. > But now it is showing as cubic box when I see the result after using > trajconv (additionally some part of the protein is out of the box). This could only be a visualization glitch. Try using trjconv options. amit > I do not have any clue how the box type has been changed or where could I > go wrong. > Please comment. > Thank you, > Cheers, > Sukesh > > -- > Sukesh Chandra Gain > TCS Innovation Labs > Tata Consultancy Services Ltd. > 'Deccan Park', Madhapur > Hyderabad 500081 > Phone: +91 40 6667 3572 > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
