[gmx-users] polymer-topology generation
Dear users, I am using Gromacs package to run the molecular simulation of a protein that is bonded to a polymer. The polymer I use has around 760 atoms and hence I am not able to generate its .itp and .gro files using PRODRG server. Is there any other way how I can generate these files of my polymer in order to use them in GROMACS?? thanking you, Regards, anand -- 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] lAM/MPI
Dear gromacs users, Our university network is LAM/MPI. I connect to the network from my office computer to submit simulation job in gromacs. In order to boot the MPI invironment I use lamboot command. $ lamboot -v lamhosts the lamhosts is a text file where I should introduce the processeros which I want to boot them and here I should include the (lnx-server) which is where I connect to, from my office computer and run the lamboot order there. Now when I want to submit simulation job I use (grompp) order which is in the path /usr/local/gromacs/bin/grompp (with the necessary options) including -np (to introduce the number of processors). Here again it seems that I should add the server to the number of processors and also it is the same for the order mpiexec . I think in this way the server will become one of the processors that my job starts to run on it and because always the server is very busy with other jobs, the speed that I get is very very low !!! please let me know if it is a way that can tell the system not to run job on the server. I think this can solve the speed problem. your answer would be greatly appreciated D.M This oprder makes the topol.tpr file -- 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] xtc file
- Original Message - From: Justin A. Lemkul jalem...@vt.edu Date: Sunday, May 23, 2010 13:49 Subject: Re: [gmx-users] xtc file To: Discussion list for GROMACS users gmx-users@gromacs.org Moeed wrote: Dear experts, I am trying to exclude all nonbonded interaction on hexane molecule. 1-For the md -rerun command I do not know how to get the input XTC file. the program is expecting rerun.xtc mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-Stack125_after_md -v output.mdrun_m As I think I have said several times, you have to do this in several steps. First, run a simulation using normal exclusions that you believe to be valid by evaluating the properties of the system. If you set nstxtcout 0 in your .mdp file, you will get a .xtc trajectory file (.xtc output is off by default - you must specify that you want it). After you have done this, use mdrun -rerun on this trajectory and whatever modified topology you have created. More precisely, mdrun -rerun will take any trajectory file, as can be seen by inspecting mdrun -h. There is no need to create an XTC file. There is a need to tell the previous mdrun to write positions when you want them to be available for the rerun, either with nstxout or nstxtcout. More specifically: 1. mdrun -deffnm md_no_excl 2. grompp to create new .tpr file with special exclusions 3. mdrun -rerun md_no_excl.xtc -s md_with_new_excl.tpr Thus, new energies will be calculated from a sensible trajectory. 2-Can you please check exclsusions directive in top file. I have used also nrexcl 5 in molecule top. does this make sense given that I have defined all the possible exclusions in 19 lines. Much of what you have defined is redundant. If you have nrexcl = 5 that means nonbonded interactions between atoms up to 5 bonds away are excluded already, so lines like 19 20 are unnecessary. Yep, use one approach or the other. Both won't hurt, but are redundant and error-prone. Mark snip All of the information I deleted is unnecessary. I appreciate that you are trying to be thorough, but long emails with excess detail dilute the information that is really needed. [ moleculetype ] ; Name nrexcl Hexane 5 Not a bad approach, but... [ exclusions ] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 7 8 9 10 11 12 13 14 15 16 17 18 19 20 8 9 10 11 12 13 14 15 16 17 18 19 20 9 10 11 12 13 14 15 16 17 18 19 20 10 11 12 13 14 15 16 17 18 19 20 11 12 13 14 15 16 17 18 19 20 12 13 14 15 16 17 18 19 20 13 14 15 16 17 18 19 20 14 15 16 17 18 19 20 15 16 17 18 19 20 16 17 18 19 20 17 18 19 20 18 19 20 19 20 ...why all the redundancy? Much of what you have here is already encompassed by the value of nrexcl. Actually, if you set nrexcl = 7, you don't have to create an [exclusions] section at all! There are no atoms more than 7 bonds away from each other in hexane, right? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-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] lAM/MPI
- Original Message - From: delara aghaie d_agh...@yahoo.com Date: Sunday, May 23, 2010 18:15 Subject: [gmx-users] lAM/MPI To: gmx-users@gromacs.org --- | Dear gromacs users, Our university network is LAM/MPI. I connect to the network from my office computer to submit simulation job in gromacs. In order to boot the MPI invironment I use lamboot command. $ lamboot -v lamhosts the lamhosts is a text file where I should introduce the processeros which I want to boot them and here I should include the (lnx-server) which is where I connect to, from my office computer and run the lamboot order there. Now when I want to submit simulation job I use (grompp) order which is in the path /usr/local/gromacs/bin/grompp (with the necessary options) including -np (to introduce the number of processors). Thus you're using GROMACS 3.x, which is long superseded. Unless you know of a scientific reason for continuing to use it, you will get much better performance from GROMACS 4.0.7. More to the point, grompp is not the simulation. It prepares the simulation input. The .tpr file is binary-portable. You can create that file anywhere, copy it to the compute machine, and then use mpirun_mpi to run it. Here again it seems that I should add the server to the number of processors and also it is the same for the order mpiexec . Unlikely. I think in this way the server will become one of the processors that my job starts to run on it and because always the server is very busy with other jobs, the speed that I get is very very low !!! Sure, so you don't want to do it. please let me know if it is a way that can tell the system not to run job on the server. I think this can solve the speed problem. This will be a standard problem (independent of GROMACS), for which the administrators for your compute environment will have a standard solution. Talk to them. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] polymer-topology generation
P.R.Anand Narayanan wrote: Dear users, I am using Gromacs package to run the molecular simulation of a protein that is bonded to a polymer. The polymer I use has around 760 atoms and hence I am not able to generate its .itp and .gro files using PRODRG server. Is there any other way how I can generate these files of my polymer in order to use them in GROMACS?? You can find some general advice here: http://www.gromacs.org/Documentation/How-tos/Polymers -Justin thanking you, Regards, anand -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Topology files for OPLSAA and RESP charges
Dear GROMACS users, I'm trying to start running jobs using RESP charges and OPLSAA force field but I am facing problems to generate the RESP charges and the topology files for the OPLSAA force field. Does someone knows a software to calculate the RESP charges for the ligands and/or, also, to generate the .itp files for OPLSAA ? With the best regards, Tanos C. C. Franca. -- 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] Polymer simulation help and suggestions
Hello all, I have just started working with GROMACS and simulation in general. I will be doing simulation of PEO with various ions and need a little help. I have read a great deal of the documentation and now edited the appropriate .rtp and.itp files to generate my polymer from a .pdb file using pdb2gmx and it seems to be generating my topology and .gro files correctly. My question is if I wish to keep a static bond length do I address this in the bond information or is there something in the .mdp file that will address this? I also would like some suggestions for a few other things. To make my preliminary polymer I used a molecular modeling/editor program called Avogadro but was wondering if there is something better to use to create the random walk long chain polymer? Also, I was just going to create my own ion files and use genion to incorporate those into the simulation but didn't know if this was the best way to do this. And lastly when I need to create a multiple polymer simulation my plan was to use genconf and generate a crystal with the appropriate number of polymers and then just heat it up to melt it. This seems to be a good way to do it however, another person in my group who used NAMD used a program called PackMol and had some success and was wondering if anyone else had used this program and would recommend this route? Thank you in advanced. Regards, Caleb -- 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] Topology files for OPLSAA and RESP charges
- Original Message - From: Tanos C. C. Franca ta...@ime.eb.br Date: Monday, May 24, 2010 1:03 Subject: [gmx-users] Topology files for OPLSAA and RESP charges To: gmx-users@gromacs.org Dear GROMACS users, I'm trying to start running jobs using RESP charges and OPLSAA force field but I am facing problems to generate the RESP charges and the topology files for the OPLSAA force field. Does someone knows a software to calculate the RESP charges for the ligands and/or, also, to generate the .itp files for OPLSAA ? The general advice is here: http://www.gromacs.org/Documentation/How-tos/Parametrization. I am not aware of an OPLSAA-specific helper tool. Be wary of presupposing that use of RESP is correct for OPLSAA. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polymer simulation help and suggestions
Caleb Tormey wrote: Hello all, I have just started working with GROMACS and simulation in general. I will be doing simulation of PEO with various ions and need a little help. I have read a great deal of the documentation and now edited the appropriate .rtp and.itp files to generate my polymer from a .pdb file using pdb2gmx and it seems to be generating my topology and .gro files correctly. My question is if I wish to keep a static bond length do I address this in the bond information or is there something in the .mdp file that will address this? Use the constraints keyword in your .mdp file. See the manual. I also would like some suggestions for a few other things. To make my preliminary polymer I used a molecular modeling/editor program called Avogadro but was wondering if there is something better to use to create the random walk long chain polymer? There are several programs that can build molecules, like xLeap (part of AmberTools) and even VMD has some capabilities for building molecules. I don't know about polymers specifically. Also, I was just going to create my own ion files and use genion to incorporate those into the simulation but didn't know if this was the best way to do this. To what files are you referring? Are you introducing new parameters of some sort? Be aware that pre-defined ion parameters are included as part of all the force field parameter sets packaged with Gromacs, so any new parameters must be validated before being used. And lastly when I need to create a multiple polymer simulation my plan was to use genconf and generate a crystal with the appropriate number of polymers and then just heat it up to melt it. This seems to be a good way to do it however, another person in my group who used NAMD used a program called PackMol and had some success and was wondering if anyone else had used this program and would recommend this route? Either way should work fine. PackMol does a good job of generating initial configurations given geometrical constraints, but your procedure should work if you do sufficient heating to change the initial structure. -Justin Thank you in advanced. Regards, Caleb -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] tpbconv subset
I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your tpx file, or when you want to make e.g. a pure Ca tpx file. WARNING: this tpx file is not fully functional. -- 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] tpbconv subset
John Shultz wrote: I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions If you have a .tpr file, then the .mdp file is a step backwards. You don't need it. Assuming you want to do some sort of re-run procedure, you simply have to run: mdrun -s subset.tpr -rerun original.xtc (where original.xtc is your trajectory file that contains the same subset of atoms as subset.tpr) -Justin http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your tpx file, or when you want to make e.g. a pure Ca tpx file. WARNING: this tpx file is not fully functional. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tpbconv subset
Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions If you have a .tpr file, then the .mdp file is a step backwards. You don't need it. Assuming you want to do some sort of re-run procedure, you simply have to run: mdrun -s subset.tpr -rerun original.xtc (where original.xtc is your trajectory file that contains the same subset of atoms as subset.tpr) -Justin http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your tpx file, or when you want to make e.g. a pure Ca tpx file. WARNING: this tpx file is not fully functional. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] tpbconv subset
John Shultz wrote: Justin, Only problem is I need to change this parameter energygrps to track the energy on specific groups in the simulation. Is there a way to modify the simulation parameters to track these energies? Modify the .mdp file the way you need to, create a full-system .tpr file, then run it through tpbconv. -Justin On Sun, May 23, 2010 at 5:07 PM, Justin A. Lemkul jalem...@vt.edu wrote: John Shultz wrote: I want to run a subset of an original trajectory. I know how to get the tpr consisting of the subset. How do I modify the simulation with a new mdp file and then run the mdrun? I was referencing these instructions If you have a .tpr file, then the .mdp file is a step backwards. You don't need it. Assuming you want to do some sort of re-run procedure, you simply have to run: mdrun -s subset.tpr -rerun original.xtc (where original.xtc is your trajectory file that contains the same subset of atoms as subset.tpr) -Justin http://manual.gromacs.org/current/online/tpbconv.html 3nd. by creating a tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your tpx file, or when you want to make e.g. a pure Ca tpx file. WARNING: this tpx file is not fully functional. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polymer simulation help and suggestions
Justin, Thank you for your response. My simulation will involve around 30 chains of polymer along with varying amounts of different salts. For instance LiPF6, LiClO4 and larger molecules like [1,3-dimethylimidazolium]PF6 and I am looking for the best way to incorporate these. I guess I am a little stumped as to the best method for generating these. Should I make separate .gro and topology files for these? Regards, Caleb PS. I haven't researched this part as much so it is possible this has already been answered and I just haven't come across this. On Sun, May 23, 2010 at 10:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: Caleb Tormey wrote: Hello all, I have just started working with GROMACS and simulation in general. I will be doing simulation of PEO with various ions and need a little help. I have read a great deal of the documentation and now edited the appropriate .rtp and.itp files to generate my polymer from a .pdb file using pdb2gmx and it seems to be generating my topology and .gro files correctly. My question is if I wish to keep a static bond length do I address this in the bond information or is there something in the .mdp file that will address this? Use the constraints keyword in your .mdp file. See the manual. I also would like some suggestions for a few other things. To make my preliminary polymer I used a molecular modeling/editor program called Avogadro but was wondering if there is something better to use to create the random walk long chain polymer? There are several programs that can build molecules, like xLeap (part of AmberTools) and even VMD has some capabilities for building molecules. I don't know about polymers specifically. Also, I was just going to create my own ion files and use genion to incorporate those into the simulation but didn't know if this was the best way to do this. To what files are you referring? Are you introducing new parameters of some sort? Be aware that pre-defined ion parameters are included as part of all the force field parameter sets packaged with Gromacs, so any new parameters must be validated before being used. And lastly when I need to create a multiple polymer simulation my plan was to use genconf and generate a crystal with the appropriate number of polymers and then just heat it up to melt it. This seems to be a good way to do it however, another person in my group who used NAMD used a program called PackMol and had some success and was wondering if anyone else had used this program and would recommend this route? Either way should work fine. PackMol does a good job of generating initial configurations given geometrical constraints, but your procedure should work if you do sufficient heating to change the initial structure. -Justin Thank you in advanced. Regards, Caleb -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polymer simulation help and suggestions
Caleb Tormey wrote: Justin, Thank you for your response. My simulation will involve around 30 chains of polymer along with varying amounts of different salts. For instance LiPF6, LiClO4 and larger molecules like [1,3-dimethylimidazolium]PF6 and I am looking for the best way to incorporate these. I guess I am a little stumped as to the best method for generating these. Should I make separate .gro and topology files for these? Yes. You won't be able to add these polyatomic ions with genion. You will have to insert them with genbox -ci -nmol instead, then #include the relevant .itp files into your .top file. Parameterization of these compounds will not be trivial. You should be prepared for significant effort to develop these parameters for the force field you've chosen, unless they've already been developed and validated. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Regards, Caleb PS. I haven't researched this part as much so it is possible this has already been answered and I just haven't come across this. On Sun, May 23, 2010 at 10:47 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Caleb Tormey wrote: Hello all, I have just started working with GROMACS and simulation in general. I will be doing simulation of PEO with various ions and need a little help. I have read a great deal of the documentation and now edited the appropriate .rtp and.itp files to generate my polymer from a .pdb file using pdb2gmx and it seems to be generating my topology and .gro files correctly. My question is if I wish to keep a static bond length do I address this in the bond information or is there something in the .mdp file that will address this? Use the constraints keyword in your .mdp file. See the manual. I also would like some suggestions for a few other things. To make my preliminary polymer I used a molecular modeling/editor program called Avogadro but was wondering if there is something better to use to create the random walk long chain polymer? There are several programs that can build molecules, like xLeap (part of AmberTools) and even VMD has some capabilities for building molecules. I don't know about polymers specifically. Also, I was just going to create my own ion files and use genion to incorporate those into the simulation but didn't know if this was the best way to do this. To what files are you referring? Are you introducing new parameters of some sort? Be aware that pre-defined ion parameters are included as part of all the force field parameter sets packaged with Gromacs, so any new parameters must be validated before being used. And lastly when I need to create a multiple polymer simulation my plan was to use genconf and generate a crystal with the appropriate number of polymers and then just heat it up to melt it. This seems to be a good way to do it however, another person in my group who used NAMD used a program called PackMol and had some success and was wondering if anyone else had used this program and would recommend this route? Either way should work fine. PackMol does a good job of generating initial configurations given geometrical constraints, but your procedure should work if you do sufficient heating to change the initial structure. -Justin Thank you in advanced. Regards, Caleb -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post
[gmx-users] implicit solvent in CVS
Dear all: I know this question has been asked many times, but it's still tempting for me to ask it again ;-). Could any one suggest a mdp file, including the proper parameter setting, for implicit solvent simulation in gromacs? From all the clues I gathered (the roadmap, the source code), it seems to me that implicit solvent is already full supported, but just not officially released. I really want to see whether this could speed up my calculation dramatically, since it's not always true that implicit solvent simulation would run faster. Thanks very much, Bin -- 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] tip5p in ffcharmm
Dear gromacs users, I could not able to use tip5p water model with charmm force field. If anybody tried successfully, please help me. Thank you. with regards, Rama -- 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] tip5p in ffcharmm
- Original Message - From: Ramachandran G gtr...@gmail.com Date: Monday, May 24, 2010 12:03 Subject: [gmx-users] tip5p in ffcharmm To: gmx-users@gromacs.org Dear gromacs users, I could not able to use tip5p water model with charmm force field. If anybody tried successfully, please help me. This is not likely to get any useful help. Tell us what you did and why you think it didn't work :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy.edr retrieves deltaG = 0 KJ/mol using g_lie
Dear Gromacs users, I ran a production MD simulation on a ligand in a water box. I used NVT with coloumb and vdw cut-offs and avoided using PME. I analyzed the .edr file using g_lie after the simulation was finished, I found that at all the time steps, the energy was 0 KJ/mol, is that normal? How come the energy of the system is 0? ' I am including both the simulation mdp file and the output of g_lie for inspection... I would appreciate if I could get any feedback about the reasons for this problem. Regards Hassan Shallal University of the Pacific Stockton, CA 95211 The mdb file: -- ;RUN CONTROL PARAMETERS = integrator = md ; production tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) dt = 0.002; ps ! nsteps = 250 ; total 5 ns. nstcomm = 1; frequency for center of mass motion removal ;OUTPUT FREQUENCY OPRIONS FOR COORDINATES, VELOCITIES, AND FORCES = (because this is equilibration, we don't want to waste hard disk storgae space) nstxout = 1000; frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout = 1000; frequency to write velocities to output trajectory, the last velocities are always written nstfout = 0; frequency to write forces to output trajectory. ;OUTPUT FREQUENCY OPRIONS FOR ENERGIES = nstlog = 2500 ; frequency to write energies to log file, the last energies are always written nstenergy= 1000 ; frequency to write energies to energy file, the last energies are always written ;NEIGHBOR SEARCHING PARAMETERS = nstlist = 10 ; neighbor list update frequency ns_type = grid ; ns algorithm (simple or grid) pbc = xyz ; periodic boundary conditions (xyz or none) rlist = 1; cut-off distance of the short-range neighbor list (nm) domain-decomposition = no ;OUTPUT FREQUENCY AND PRESISION FOR XTC FILES = nstxtcout= 5000 ; frequency to write coordinates to xtc trajectory (STEPS) xtc-precision= 1000 ; precision to write to xtc trajectory energygrps = SOL UNK ;OPTIONS FOR ELECTROSTATIC AND VDW = coulombtype = Cut-off ; method of doing electrostatics (Twin range cut-off's with neighborlist cut-off rlist and Coulomb cut-off rcoulomb, where rcoulomb ? rlist.) rcoulomb_switch = 0; where to start switching the Coulomb potential (nm) rcoulomb= 1; distance for Coulomb cut-off (nm) epsilon_r = 1; the relative dielectric constant (1 or zero, if zero, means infinity) vdwtype = Cut-off ; method of doing VDW (Twin range cut-off's with neighbor list cut-off rlist and VdW cut-off rvdw, where rvdw ? rlist.) rvdw= 1; distance for LJ or Buckingham cut-off (nm) DispCorr= no ; Don't apply long range dispersion corrections for Energy and Pressure ;OPTIONS FOR TEMPERATURE COUPLING = Tcoupl = v-rescale tau_t = 0.1; time constant for coupling in ps (one for each group in tc grps), 0 means no temperature coupling tc_grps = System ; to avoid hot solvent cold solute situation ref_t = 298.15 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = no pcoupltype = isotropic ; Isotropic pressure coupling with time constant tau_p= 0.5 ; time constant for coupling in ps compressibility = 4.5e-05 ; compressibility for water at 1 atm and 300 K ref_p= 1.0 --- The .xvg g_lie output file: -- # This file was created Fri May 21 17:21:18 2010 # by the following command: # g_lie -f 4_pr_NVT.edr -o 4_pr_NVT.xvg # # g_lie is part of G R O M A C S: # # Grunge ROck MAChoS # @title LIE free energy estimate @xaxis label Time (ps) @yaxis label DGbind (kJ/mol) @TYPE xy 0 0 2 0 4 0 6 0 8 0 10 0 12 0 14 0 16 0 18 0 20 0 22 0 all the way until 5000 0 0 0
Re: [gmx-users] energy.edr retrieves deltaG = 0 KJ/mol using g_lie
Hassan Shallal wrote: Dear Gromacs users, I ran a production MD simulation on a ligand in a water box. I used NVT with coloumb and vdw cut-offs and avoided using PME. I analyzed the .edr file using g_lie after the simulation was finished, I found that at all the time steps, the energy was 0 KJ/mol, is that normal? How come the energy of the system is 0? ' I am including both the simulation mdp file and the output of g_lie for inspection... What was your g_lie command? The default values of -Elj and -Eqq are zero. Based on your energygrps (SOL and UNK), you are inherently defining the interactions between the solvent and UNK as zero unless you are setting some other value. -Justin I would appreciate if I could get any feedback about the reasons for this problem. Regards Hassan Shallal University of the Pacific Stockton, CA 95211 The mdb file: -- ;RUN CONTROL PARAMETERS = integrator = md ; production tinit = 0; starting time for your run (only makes sense for integrators md, sd and bd) dt = 0.002; ps ! nsteps = 250 ; total 5 ns. nstcomm = 1; frequency for center of mass motion removal ;OUTPUT FREQUENCY OPRIONS FOR COORDINATES, VELOCITIES, AND FORCES = (because this is equilibration, we don't want to waste hard disk storgae space) nstxout = 1000; frequency to write coordinates to output trajectory file, the last coordinates are always written nstvout = 1000; frequency to write velocities to output trajectory, the last velocities are always written nstfout = 0; frequency to write forces to output trajectory. ;OUTPUT FREQUENCY OPRIONS FOR ENERGIES = nstlog = 2500 ; frequency to write energies to log file, the last energies are always written nstenergy= 1000 ; frequency to write energies to energy file, the last energies are always written ;NEIGHBOR SEARCHING PARAMETERS = nstlist = 10 ; neighbor list update frequency ns_type = grid ; ns algorithm (simple or grid) pbc = xyz ; periodic boundary conditions (xyz or none) rlist = 1; cut-off distance of the short-range neighbor list (nm) domain-decomposition = no ;OUTPUT FREQUENCY AND PRESISION FOR XTC FILES = nstxtcout= 5000 ; frequency to write coordinates to xtc trajectory (STEPS) xtc-precision= 1000 ; precision to write to xtc trajectory energygrps = SOL UNK ;OPTIONS FOR ELECTROSTATIC AND VDW = coulombtype = Cut-off ; method of doing electrostatics (Twin range cut-off’s with neighborlist cut-off rlist and Coulomb cut-off rcoulomb, where rcoulomb ≥ rlist.) rcoulomb_switch = 0; where to start switching the Coulomb potential (nm) rcoulomb= 1; distance for Coulomb cut-off (nm) epsilon_r = 1; the relative dielectric constant (1 or zero, if zero, means infinity) vdwtype = Cut-off ; method of doing VDW (Twin range cut-off’s with neighbor list cut-off rlist and VdW cut-off rvdw, where rvdw ≥ rlist.) rvdw= 1; distance for LJ or Buckingham cut-off (nm) DispCorr= no ; Don't apply long range dispersion corrections for Energy and Pressure ;OPTIONS FOR TEMPERATURE COUPLING = Tcoupl = v-rescale tau_t = 0.1; time constant for coupling in ps (one for each group in tc grps), 0 means no temperature coupling tc_grps = System ; to avoid hot solvent cold solute situation ref_t = 298.15 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = no pcoupltype = isotropic ; Isotropic pressure coupling with time constant tau_p= 0.5 ; time constant for coupling in ps compressibility = 4.5e-05 ; compressibility for water at 1 atm and 300 K ref_p= 1.0 --- The .xvg g_lie output file: -- # This file was created Fri May 21 17:21:18 2010 # by the following command: # g_lie -f 4_pr_NVT.edr -o 4_pr_NVT.xvg # # g_lie is part of G R O M A C S: # # Grunge ROck MAChoS # @title LIE free energy estimate @xaxis label Time (ps) @yaxis label DGbind (kJ/mol) @TYPE xy 0 0 2 0 4 0 6 0
[gmx-users] simulation crashed because of LINCS error
Hello All, With regard to my previous post http://www.mail-archive.com/gmx-users@gromacs.org/msg30557.html I have done postion restrained energy minimisation using POSRES.itp file obtained from pdb2gmx. so that there should not be any large change in the strucutre of the protein. And after that I did equilbration using following mdp file title = protein cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 After this, I put the molecule for simulation using the following .mdp file title = protein cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 50 ; total 1000 ps, 1 ns. nstcomm = 1 nstxout = 500 ; collect data every 1 ps nstvout = 0 nstfout = 0 nstlist = 5 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 30 ; Pressure coupling is on Pcoupl = berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 but simulation has crashed showing the error too many Too many LINCS warnings (1000) I checked previous posts, it is given that it may be due to incomplete equilibration or putting so many constraints. So can you please help me in correcting it. Thanks and regards. -- Sonali Dhindwal -- 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] Density question
Dear Gromacs Users, I run an MD simulation of a pure solvent and found out that the density of the solvent deviated a little bit from the actual experimental data. MD density is 880g/ml and the experimental data is 866g/ml. Is this reasonable for toluene solvent molecules. I have a hard time of lowering the density to the experimental value. I am using ff53a6 gromos force field with rlist=rvwd=rcoulomb=0.9nm. Is there any advice on this or it is OK. Thank you Rob -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
