[gmx-users] NPT - umbrella sampling
Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined). I would like to run NPT before running umbrella sampling simulations. As far I see Justin in his tutorial NPT and umbrella sampling mdp files looks the same which means you did not restrain whole protein in your system during NPT? Why? Shall rund NPT withou restraining protein and ligand before umbrella sampling in each window? Thank you, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?
I am not referring to any drift of the whole system, but to the diffusion of the lipid bilayer only. Diffusion of molecules in water is to be expected given sufficient time. I wonder what is a reasonable restraint to keep the center of mass of the membrane at Z=0.0 -Jose On Wed, Feb 22, 2012 at 9:04 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/02/2012 10:26 AM, Jose Borreguero wrote: Dear GROMACS users, While simulating a DLPC membrane, I noticed that it tends to diffuse along the normal (Z-axis) component. Is there a 'standard' restrain that is used to prevent such diffusion? The first option I thought was to restrain the center of mass of the whole membrane along the Z-axis, but I don't know what is a reasonable value for the force constant. If anyone has any experience dealing with this kind of problem, please do reply. Diffusion of the center of mass of the whole system is something that can be removed by an existing mechanism. See manual 7.3.3 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error note
Dear friends, iam getting this note while doing pressure coupling of protein-ligand complex. can anybody help me how to handle this?? The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Thanks -- *Ramya.LN* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT - umbrella sampling
Steven Neumann wrote: Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined). I would like to run NPT before running umbrella sampling simulations. As far I see Justin in his tutorial NPT and umbrella sampling mdp files looks the same which means you did not restrain whole protein in your system during NPT? Why? The system at hand was very robust and as such, complete restraints were not necessary. Please do not adhere strictly to the umbrella sampling tutorial; there are elements of it that may not be generally applicable (and I'm fairly sure there are warnings of this in the tutorial). It is a simple example designed to provide the conceptual and practical basis for such simulations. Shall rund NPT withou restraining protein and ligand before umbrella sampling in each window? Do what makes sense in your case. Typically, position restraints are applied during equilibration. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling - gen_temp
Steven Neumann wrote: Dear Justin, Can I ask you why didnt you use in your mdp files for umbrella sampling (both MD and NPT): gen_temp = 310 ; temperature for Maxwell distribution I wasn't generating velocities in those steps, and as such, setting gen_temp was unnecessary. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT - umbrella sampling
On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined). I would like to run NPT before running umbrella sampling simulations. As far I see Justin in his tutorial NPT and umbrella sampling mdp files looks the same which means you did not restrain whole protein in your system during NPT? Why? The system at hand was very robust and as such, complete restraints were not necessary. Please do not adhere strictly to the umbrella sampling tutorial; there are elements of it that may not be generally applicable (and I'm fairly sure there are warnings of this in the tutorial). It is a simple example designed to provide the conceptual and practical basis for such simulations. Shall rund NPT withou restraining protein and ligand before umbrella sampling in each window? Do what makes sense in your case. Typically, position restraints are applied during equilibration. -Justin Maybe I asked my qestion not directly. Why during the equilibration of your system (tutorial) NPT before umbrella sampling in each window you restarined only Chain B like in further umbrella samplin (your mdp files of NPT and MD are the same) instead of restraining all chains as it should be during the equilibration? Steven -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NPT - umbrella sampling
Steven Neumann wrote: On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined). I would like to run NPT before running umbrella sampling simulations. As far I see Justin in his tutorial NPT and umbrella sampling mdp files looks the same which means you did not restrain whole protein in your system during NPT? Why? The system at hand was very robust and as such, complete restraints were not necessary. Please do not adhere strictly to the umbrella sampling tutorial; there are elements of it that may not be generally applicable (and I'm fairly sure there are warnings of this in the tutorial). It is a simple example designed to provide the conceptual and practical basis for such simulations. Shall rund NPT withou restraining protein and ligand before umbrella sampling in each window? Do what makes sense in your case. Typically, position restraints are applied during equilibration. -Justin Maybe I asked my qestion not directly. Why during the equilibration of your system (tutorial) NPT before umbrella sampling in each window you restarined only Chain B like in further umbrella samplin (your mdp files of NPT and MD are the same) instead of restraining all chains as it should be during the equilibration? What should be depends on the system. In my case, the structures were extremely robust and did not require full restraints to achieve adequate equilibration. This is not generally true and full restraints are normally applied. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error note
RAMYA NAGA wrote: Dear friends, iam getting this note while doing pressure coupling of protein-ligand complex. can anybody help me how to handle this?? The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. The error message explains what is wrong and how it should be fixed. Charge groups should be small. You have one that is very large. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?
Jose Borreguero wrote: I am not referring to any drift of the whole system, but to the diffusion of the lipid bilayer only. Diffusion of molecules in water is to be expected given sufficient time. I wonder what is a reasonable restraint to keep the center of mass of the membrane at Z=0.0 COM motion removal should take care of this. I do not see how the bilayer would be the only species that moves; the water molecules are not static. They too are moving in z along with the membrane. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error note
Hi Justin I saw this and had a question. How important is it for a charge group to be neutral? In one of my systems I model a solvent of crown ethers using an all atom model. The smallest neutral unit comprises a CH2-O-CH2 (7 atoms). I have used this as a charge group to and get no warnings. Cheers Gavin Justin A. Lemkul wrote: RAMYA NAGA wrote: Dear friends, iam getting this note while doing pressure coupling of protein-ligand complex. can anybody help me how to handle this?? The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. The error message explains what is wrong and how it should be fixed. Charge groups should be small. You have one that is very large. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error note
Gavin Melaugh wrote: Hi Justin I saw this and had a question. How important is it for a charge group to be neutral? It isn't. Conventional use dictates that the charge group bear an integral charge. With PME, this is not necessary. Many force fields do not use charge groups at all (i.e., single-atom charge groups). In one of my systems I model a solvent of crown ethers using an all atom model. The smallest neutral unit comprises a CH2-O-CH2 (7 atoms). I have used this as a charge group to and get no warnings. The only implication I can think of would be in neighbor searching. If the group is large, then short-range forces may not be calculated accurately. The warning from grompp was a recent addition to the code; if you're using an older version you may not have triggered it. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?
On 23/02/2012 10:27 PM, Jose Borreguero wrote: I am not referring to any drift of the whole system, but to the diffusion of the lipid bilayer only. Diffusion of molecules in water is to be expected given sufficient time. I wonder what is a reasonable restraint to keep the center of mass of the membrane at Z=0.0 You can't have the bilayer drift unless the water drifts with it or through it. The former is more likely, thus you likely have COM motion. Mark -Jose On Wed, Feb 22, 2012 at 9:04 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/02/2012 10:26 AM, Jose Borreguero wrote: Dear GROMACS users, While simulating a DLPC membrane, I noticed that it tends to diffuse along the normal (Z-axis) component. Is there a 'standard' restrain that is used to prevent such diffusion? The first option I thought was to restrain the center of mass of the whole membrane along the Z-axis, but I don't know what is a reasonable value for the force constant. If anyone has any experience dealing with this kind of problem, please do reply. Diffusion of the center of mass of the whole system is something that can be removed by an existing mechanism. See manual 7.3.3 Mark -- gmx-users mailing list gmx-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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error note
I am using 4.5.5 Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I saw this and had a question. How important is it for a charge group to be neutral? It isn't. Conventional use dictates that the charge group bear an integral charge. With PME, this is not necessary. Many force fields do not use charge groups at all (i.e., single-atom charge groups). In one of my systems I model a solvent of crown ethers using an all atom model. The smallest neutral unit comprises a CH2-O-CH2 (7 atoms). I have used this as a charge group to and get no warnings. The only implication I can think of would be in neighbor searching. If the group is large, then short-range forces may not be calculated accurately. The warning from grompp was a recent addition to the code; if you're using an older version you may not have triggered it. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error note
Gavin Melaugh wrote: I am using 4.5.5 The warning is only triggered if the charge group is 10 atoms or larger. Why this is the threshold, I can't say. I didn't write the code ;) You may still want to do some tests with smaller charge groups to make sure the changes do not produce significantly different energies. -Justin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I saw this and had a question. How important is it for a charge group to be neutral? It isn't. Conventional use dictates that the charge group bear an integral charge. With PME, this is not necessary. Many force fields do not use charge groups at all (i.e., single-atom charge groups). In one of my systems I model a solvent of crown ethers using an all atom model. The smallest neutral unit comprises a CH2-O-CH2 (7 atoms). I have used this as a charge group to and get no warnings. The only implication I can think of would be in neighbor searching. If the group is large, then short-range forces may not be calculated accurately. The warning from grompp was a recent addition to the code; if you're using an older version you may not have triggered it. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] what restraint can I use to prevent membrane diffusion along the Z-axis?
Yes, the water certainly drifts along with the membrane. Umm, it is safe to remove the COM momentum in an NPT (Langevin+piston) simulation? Later I want to do a steered dynamics simulation for this system. The external applied force will certainly produce a nonzero net momentum. Is it safe to remove the COM momentum in this case? -Jose On Thu, Feb 23, 2012 at 8:35 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/02/2012 10:27 PM, Jose Borreguero wrote: I am not referring to any drift of the whole system, but to the diffusion of the lipid bilayer only. Diffusion of molecules in water is to be expected given sufficient time. I wonder what is a reasonable restraint to keep the center of mass of the membrane at Z=0.0 You can't have the bilayer drift unless the water drifts with it or through it. The former is more likely, thus you likely have COM motion. Mark -Jose On Wed, Feb 22, 2012 at 9:04 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/02/2012 10:26 AM, Jose Borreguero wrote: Dear GROMACS users, While simulating a DLPC membrane, I noticed that it tends to diffuse along the normal (Z-axis) component. Is there a 'standard' restrain that is used to prevent such diffusion? The first option I thought was to restrain the center of mass of the whole membrane along the Z-axis, but I don't know what is a reasonable value for the force constant. If anyone has any experience dealing with this kind of problem, please do reply. Diffusion of the center of mass of the whole system is something that can be removed by an existing mechanism. See manual 7.3.3 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Options to be specified for the buckingham potential
Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp file as [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no0.0 1.0 Here my doubt are 1) Am i using correct options for the combination-rule and fudgeQQ ? 2) what i understood from manual is usage of option 'yes' for the gen-pairs is not allowed with the buckingham potential and fudgeLj is used only when gen-pairs is set to 'yes' is my understanding correct? Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Determining energies between a solute and solvent
Hello everyone, Is it possible to see the energy (LJ, Cou) for simply the solute interacting with the solvent? For example, g_energy will calculate all the energies for the entire system interactions which include solvent-solvent interactions. I would simply like the solute-solvent interactions or possibly simply the solvent-solvent interaction energies. I see g_enemat as a possible function to use. Is this the best way? Thanks. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Determining energies between a solute and solvent
Fabian Casteblanco wrote: Hello everyone, Is it possible to see the energy (LJ, Cou) for simply the solute interacting with the solvent? Short-range nonbonded interactions can be decomposed using proper energygrps in the .mdp file. For example, g_energy will calculate all the energies for the entire system interactions which include solvent-solvent interactions. I would simply like the solute-solvent interactions or possibly simply the solvent-solvent interaction energies. I see g_enemat as a possible function to use. Is this the best way? Perhaps, but g_enemat also requires that energygrps are specified when running the simulation. Otherwise, the applicable terms in the .edr file are not decomposed. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Determining energies between a solute and solvent
Thanks. So before I run the simulation, I must use energygrps (for example: energygrps: Protein SOL) in my md.mdp file so that it knows to write down specific interactions between the two groups. Will then it simply appear when I later run g_energy? -Fabian - Short-range nonbonded interactions can be decomposed using proper energygrps in the .mdp file. Perhaps, but g_enemat also requires that energygrps are specified when running the simulation. Otherwise, the applicable terms in the .edr file are not decomposed. -Justin On Thu, Feb 23, 2012 at 1:56 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello everyone, Is it possible to see the energy (LJ, Cou) for simply the solute interacting with the solvent? For example, g_energy will calculate all the energies for the entire system interactions which include solvent-solvent interactions. I would simply like the solute-solvent interactions or possibly simply the solvent-solvent interaction energies. I see g_enemat as a possible function to use. Is this the best way? Thanks. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Determining energies between a solute and solvent
Fabian Casteblanco wrote: Thanks. So before I run the simulation, I must use energygrps (for example: energygrps: Protein SOL) in my md.mdp file so that it knows to write down specific interactions between the two groups. Will then it simply appear when I later run g_energy? Yes. -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Positive Coul. recip. term
Dear all, I am trying to equilibrate a solvent of pure ionic liquid. The system keeps exploding (after 2-5 ns) and I am not sure why, though I believe coulombic interactions are to blame. This is because the Coul-SR term is negative, but the Coul. recip term is very positive throughout the entire run (giving the entire system a positive potential energy). I think this means that the short-range electrostatics are okay, but the long range electrostatics (calculated with PME) are not. Does anybody have any suggestions as to why this would happen? I have used the exact same PME input parameters for another ionic liquid that works just fine. They are listed below. rcoulomb = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 Thanks! Denzil Frost -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Peptide protonation inside membrane
Dear Users, when using pdb2gmx with the -inter flag, how should one manage the residues charges of a peptide which is fully embedded in a lipid bilayer? It seems that there are evidences that ARG residue remains protonated inside the membrane (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275699/). How about the HIS, LYS etc? Sorry if it's a dull question, however I found very little comments on the subject. Thanks in advance, Ricardo.-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Determining energies between a solute and solvent
Thanks. This helps. One more question, is it possible to further break down the energy interactions between a piece of a protein and another piece of the solvent? For example, if I wanted the Cou and vdw interactions specifically for an -OH group on a solvent and some chain on the solute. I know how to do this using make_ndx for g(r) plots but I don't see how you can apply it to energygrps on the *.mdp file. Thanks again for all your help. -Fabian On Thu, Feb 23, 2012 at 2:41 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Thanks. So before I run the simulation, I must use energygrps (for example: energygrps: Protein SOL) in my md.mdp file so that it knows to write down specific interactions between the two groups. Will then it simply appear when I later run g_energy? -Fabian - Short-range nonbonded interactions can be decomposed using proper energygrps in the .mdp file. Perhaps, but g_enemat also requires that energygrps are specified when running the simulation. Otherwise, the applicable terms in the .edr file are not decomposed. -Justin On Thu, Feb 23, 2012 at 1:56 PM, Fabian Casteblanco fabian.castebla...@gmail.com wrote: Hello everyone, Is it possible to see the energy (LJ, Cou) for simply the solute interacting with the solvent? For example, g_energy will calculate all the energies for the entire system interactions which include solvent-solvent interactions. I would simply like the solute-solvent interactions or possibly simply the solvent-solvent interaction energies. I see g_enemat as a possible function to use. Is this the best way? Thanks. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Determining energies between a solute and solvent
Fabian Casteblanco wrote: Thanks. This helps. One more question, is it possible to further break down the energy interactions between a piece of a protein and another piece of the solvent? For example, if I wanted the Cou and vdw interactions specifically for an -OH group on a solvent and some chain on the solute. I know how to do this using make_ndx for g(r) plots but I don't see how you can apply it to energygrps on the *.mdp file. It is possible, just a little more complicated. The use of energygrps requires that the groups be non-overlapping, so if you have some fragments you want to consider, you have to create complementary groups for all the rest, i.e.: enerygrps = fragment Protein_not_fragment sol_fragment SOL_not_sol_fragment -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Peptide protonation inside membrane
Ricardo O. S. Soares wrote: Dear Users, when using pdb2gmx with the -inter flag, how should one manage the residues charges of a peptide which is fully embedded in a lipid bilayer? It seems that there are evidences that ARG residue remains protonated inside the membrane (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275699/). How about the HIS, LYS etc? Sorry if it's a dull question, however I found very little comments on the subject. There is quite a lot in the literature about pKa shifting based on different microenvironments. There are also a number of tools available to do pKa estimates, for instance: http://biophysics.cs.vt.edu/ -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] rc or rlist in minimum image convention?
Hi all, My average size is 2.9 nm obtained from NPT under large pressure and now I intend to increase rc to 1.4 and rlist to 1.65 nm. I am just worried about violating minimum image convention. 1- My question is which of rc or rlist is important for minimum image convention? If its rlist then I think I have to make a bigger system. 2- Will the simulation raise warning once half of the box size rc or (rlist) ? I mean I want to make sure than over the course of simulation I am not breaching this rule. Thanks for your guidance, J. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] rc or rlist in minimum image convention?
On 24/02/2012 10:55 AM, Juliette N. wrote: Hi all, My average size is 2.9 nm obtained from NPT under large pressure and now I intend to increase rc to 1.4 and rlist to 1.65 nm. I am just worried about violating minimum image convention. That probably violates the parametrization of your force field. 1- My question is which of rc or rlist is important for minimum image convention? The larger one. See manual 3.2.2. If its rlist then I think I have to make a bigger system. 2- Will the simulation raise warning once half of the box size rc or (rlist) ? I mean I want to make sure than over the course of simulation I am not breaching this rule. Under at least some circumstances such volume changes cause fatal errors. You can check for such after the fact with g_mindist -pi Mark Thanks for your guidance, J. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Positive Coul. recip. term
On 24/02/2012 7:35 AM, Denny Frost wrote: Dear all, I am trying to equilibrate a solvent of pure ionic liquid. The system keeps exploding (after 2-5 ns) and I am not sure why, though I believe coulombic interactions are to blame. This is because the Coul-SR term is negative, but the Coul. recip term is very positive throughout the entire run (giving the entire system a positive potential energy). I think this means that the short-range electrostatics are okay, but the long range electrostatics (calculated with PME) are not. Does anybody have any suggestions as to why this would happen? I have used the exact same PME input parameters for another ionic liquid that works just fine. They are listed below. rcoulomb = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 The most likely explanation for this is a problem linking the executable, perhaps dynamically. The FFT process is then garbage which normally generates inappropriate values for Coul. recip. terms. I'd suggest re-compiling GROMACS, perhaps using static linking. You could use the GROMACS built-in fftpack for simplicity while diagnosing. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] rc or rlist in minimum image convention?
On 23 February 2012 20:07, Mark Abraham mark.abra...@anu.edu.au wrote: On 24/02/2012 10:55 AM, Juliette N. wrote: Hi all, My average size is 2.9 nm obtained from NPT under large pressure and now I intend to increase rc to 1.4 and rlist to 1.65 nm. I am just worried about violating minimum image convention. That probably violates the parametrization of your force field. Thanks Mark. You mean rc =1.4 for OPLS-AA is not appropriate? In the original OPLSAA: Optimized Intermolecular Potential Functions for Liquid Hydrocarbons I see rc of 15 A has been used for alkanes which requires rlist of around 15+2.5+17.5 A ! Please comment why I am violating parametrization? Thanks. 1- My question is which of rc or rlist is important for minimum image convention? The larger one. See manual 3.2.2. If its rlist then I think I have to make a bigger system. 2- Will the simulation raise warning once half of the box size rc or (rlist) ? I mean I want to make sure than over the course of simulation I am not breaching this rule. Under at least some circumstances such volume changes cause fatal errors. You can check for such after the fact with g_mindist -pi Alright so I dont need to worry about it if simulation crashes under such conditions.. Mark Thanks for your guidance, J. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tabulate potential
i need to add several customized potential functions into gromacs by *tabulating the potential.* However i have a question about tabulating: How many customized potential functions can i add using tabulating? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] rc or rlist in minimum image convention?
On 24/02/12, Juliette N. joojoojo...@gmail.com wrote: On 23 February 2012 20:07, Mark Abraham mark.abra...@anu.edu.au wrote: On 24/02/2012 10:55 AM, Juliette N. wrote: Hi all, My average size is 2.9 nm obtained from NPT under large pressure and now I intend to increase rc to 1.4 and rlist to 1.65 nm. I am just worried about violating minimum image convention. That probably violates the parametrization of your force field. Thanks Mark. You mean rc =1.4 for OPLS-AA is not appropriate? In the original OPLSAA: Optimized Intermolecular Potential Functions for Liquid Hydrocarbons I see rc of 15 A has been used for alkanes which requires rlist of around 15+2.5+17.5 A ! Please comment why I am violating parametrization? Thanks. It is appropriate to use a set of .mdp parameters that most closely reproduce the parametrization conditions, or other conditions that have been shown to be effective. So if you were using rc1.4 and now want to use rc=1.4, then it is likely that at least one of those choices is inappropriate. If 1.5nm was used in parameterization, then both the foregoing are probably unsuitable. The values for other rxxx parameters should be addressed in that work, and will depend on charge group size and electrostatics model. Mark 1- My question is which of rc or rlist is important for minimum image convention? The larger one. See manual 3.2.2. If its rlist then I think I have to make a bigger system. 2- Will the simulation raise warning once half of the box size rc or (rlist) ? I mean I want to make sure than over the course of simulation I am not breaching this rule. Under at least some circumstances such volume changes cause fatal errors. You can check for such after the fact with g_mindist -pi Alright so I dont need to worry about it if simulation crashes under such conditions.. Mark Thanks for your guidance, J. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tabulate potential
On 24/02/12, smith bill summerpulse2...@gmail.com wrote: i need to add several customized potential functions into gromacs by tabulating the potential. However i have a question about tabulating: How many customized potential functions can i add using tabulating? See manual 6.7.2 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Options for the buckingham potential
Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp file as [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no0.0 1.0 Here my doubt are 1) Am i using correct options for the combination-rule and fudgeQQ ? 2) what i understood from manual is usage of option 'yes' for the gen-pairs is not allowed with the buckingham potential and fudgeLj is used only when gen-pairs is set to 'yes' is my understanding correct? Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Peptide protonation inside membrane
Hi Justin, thanks, for your reply. I'm going to check H++ tools on my system. Cheers, --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. De: Justin A. Lemkul jalem...@vt.edu Para: Ricardo O. S. Soares ross_...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Quinta-feira, 23 de Fevereiro de 2012 18:07 Assunto: Re: [gmx-users] Peptide protonation inside membrane Ricardo O. S. Soares wrote: Dear Users, when using pdb2gmx with the -inter flag, how should one manage the residues charges of a peptide which is fully embedded in a lipid bilayer? It seems that there are evidences that ARG residue remains protonated inside the membrane (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275699/). How about the HIS, LYS etc? Sorry if it's a dull question, however I found very little comments on the subject. There is quite a lot in the literature about pKa shifting based on different microenvironments. There are also a number of tools available to do pKa estimates, for instance: http://biophysics.cs.vt.edu/ -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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Options for the buckingham potential
On 24/02/2012 4:06 PM, ramesh cheerla wrote: Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp file as [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no0.0 1.0 Here my doubt are 1) Am i using correct options for the combination-rule and fudgeQQ ? See 4.1.2 for combination rule. fudgeQQ effects electrostatic interactions. 2) what i understood from manual is usage of option 'yes' for the gen-pairs is not allowed with the buckingham potential and fudgeLj is used only when gen-pairs is set to 'yes' is my understanding correct? Yes. See 5.7.1 Mark Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding new residue to the the force field
Dear Mark I am very thank ful to you for your valuble suggestion. I have verified my results by changing the sigma and epsilon values in [atomtypes ] directive of the ffnonbonded.itp . Results were uneffected by changing these values. Here i have one another doubt regarding [ pairtypes ] directive, As I am using buckingham potential for the nonbonded interactions and have only A, B C values can i use zeros for the sigma and epsilon values in this directive. What i observed is results will change by changing the sigma and epsilon values in this directive. Please suggest me how can i use correct values for the sigma and epsilon in [ pairtypes ] directive. Thank you in advance. On Thu, Feb 23, 2012 at 7:32 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/02/2012 6:02 AM, ramesh cheerla wrote: Dear gromacs users, I am adding a new residue to the existing force field in gromacs for that i am using some new atom types i added these atom types to the atomtypes.atp file and ffnonbonded.itp and I am using Buckingham potential for the non-bonded interactions for that i have only A,BC values, but in the [atomtype] directive of the ffnonbonded.itp file one has to specify the sigma and epsilon values. How can i get these values ? or can i specify these values as zeros ? You will be able to use zeroes. You can verify that there's no effect by changing the values to ludicrous ones and observing that the simulation is the same. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Options for the buckingham potential
On 24/02/2012 5:15 PM, Mark Abraham wrote: On 24/02/2012 4:06 PM, ramesh cheerla wrote: Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp file as [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 0.0 1.0 Here my doubt are 1) Am i using correct options for the combination-rule and fudgeQQ ? See 4.1.2 for combination rule. Actually, 4.1.2 is wrong about the combination rule for B. See example in 5.7.1 for correct combination rule. Mark fudgeQQ effects electrostatic interactions. 2) what i understood from manual is usage of option 'yes' for the gen-pairs is not allowed with the buckingham potential and fudgeLj is used only when gen-pairs is set to 'yes' is my understanding correct? Yes. See 5.7.1 Mark Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Adding new residue to the the force field
On 24/02/2012 5:20 PM, ramesh cheerla wrote: Dear Mark I am very thank ful to you for your valuble suggestion. I have verified my results by changing the sigma and epsilon values in [atomtypes ] directive of the ffnonbonded.itp . Results were uneffected by changing these values. Here i have one another doubt regarding [ pairtypes ] directive, As I am using buckingham potential for the nonbonded interactions and have only A, B C values can i use zeros for the sigma and epsilon values in this directive. What i observed is results will change by changing the sigma and epsilon values in this directive. Please suggest me how can i use correct values for the sigma and epsilon in [ pairtypes ] directive. As I understand things, pairs for special 1-4 interactions are not used with Buckingham interactions. Looking closer at your original post, you claim to be adding a residue using Buckingham to an existing force field. No force fields distributed with GROMACS use Buckingham, so if you're trying to make both LJ and Buckingham work in the same simulation, you will be unable to succeed. Mark Thank you in advance. On Thu, Feb 23, 2012 at 7:32 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 23/02/2012 6:02 AM, ramesh cheerla wrote: Dear gromacs users, I am adding a new residue to the existing force field in gromacs for that i am using some new atom types i added these atom types to the atomtypes.atp file and ffnonbonded.itp and I am using Buckingham potential for the non-bonded interactions for that i have only A,BC values, but in the [atomtype] directive of the ffnonbonded.itp file one has to specify the sigma and epsilon values. How can i get these values ? or can i specify these values as zeros ? You will be able to use zeroes. You can verify that there's no effect by changing the values to ludicrous ones and observing that the simulation is the same. Mark -- gmx-users mailing list gmx-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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Positive Coul. recip. term
On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote: Dear all, I am trying to equilibrate a solvent of pure ionic liquid. The system keeps exploding (after 2-5 ns) and I am not sure why, though I believe coulombic interactions are to blame. This is because the Coul-SR term is negative, but the Coul. recip term is very positive throughout the entire run (giving the entire system a positive potential energy). I think this means that the short-range electrostatics are okay, but the long range electrostatics (calculated with PME) are not. Does anybody have any suggestions as to why this would happen? I have used the exact same PME input parameters for another ionic liquid that works just fine. They are listed below. rcoulomb = 1.2 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 Depends on the force field you are using. Perhaps it ist not validated for the ionic liquid you want to study. It is especially strange, that it takes so long for your system to blow up. Moreoever I would try to optimize the PME settings with the tools, g_tune_pme and g_pme_error, which give you performance and accuracy of the parameters, respectively. So perhaps with some more information I can provide more help. /Flo Thanks! Denzil Frost -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Internal water in the membrane receptor
Up! :) Please provide me with the best sollution of my problem! I just want to copy some water mollecules from X-ray structure to my model and place it in the identical possitions inside the TM budle of my protein. What are the most trivial way to solve this task? James 2012/2/22 James Starlight jmsstarli...@gmail.com Dear Gromacs Users! I want to perform simulation of the membrane receptor in the membtane environment. There are some evidence about precense of the functional-relevant internal water mollecules in the transmembrane alpha-helix bundle of the receptor. I want to take into account that internal water in my model. I have coordinates of the X-ray structures wich have all that water. Also I have perfect model of the same protein wich have not that water but have full-length structure ( there are some missing residues in the X-ray structures- e.g in the loop regions). So what the best way to build system would be in my case? 1- Should I use X-ray structure where internal water has already present and build missing loops via model software ? How I could preserve the internal waters in that starting structure when this structure will be processed by pdb2gmx ? 2- Or the best way is to incorporate all waters in the model of my protein ? If this aproach could be better what is the simplest way to transfer exact coordinates of water in that holo model ? ) Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Internal water in the membrane receptor
On 24/02/2012 6:31 PM, James Starlight wrote: Up! :) Please provide me with the best sollution of my problem! I just want to copy some water mollecules from X-ray structure to my model and place it in the identical possitions inside the TM budle of my protein. What are the most trivial way to solve this task? You have a non-trivial problem. You can either build the model on the structure that has the waters (pdb2gmx doesn't strip water, IIRC), or work out some geometric criteria for placing the waters afterwards. Not every problem has an existing tool for its solution. Mark James 2012/2/22 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com Dear Gromacs Users! I want to perform simulation of the membrane receptor in the membtane environment. There are some evidence about precense of the functional-relevant internal water mollecules in the transmembrane alpha-helix bundle of the receptor. I want to take into account that internal water in my model. I have coordinates of the X-ray structures wich have all that water. Also I have perfect model of the same protein wich have not that water but have full-length structure ( there are some missing residues in the X-ray structures- e.g in the loop regions). So what the best way to build system would be in my case? 1- Should I use X-ray structure where internal water has already present and build missing loops via model software ? How I could preserve the internal waters in that starting structure when this structure will be processed by pdb2gmx ? 2- Or the best way is to incorporate all waters in the model of my protein ? If this aproach could be better what is the simplest way to transfer exact coordinates of water in that holo model ? ) Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Internal water in the membrane receptor
Mark, what about the next sollution firstly I'll align both of my structures ( x-ray with water and another my model without water) than I'll copy aligned water from first structure to my model in the bottom of the GRO file. than I'll minimise this editted structure to relax side chains of the residues wich are in contact with the new waters Might this aproach be usefull? Commonly I use it to prepare protein-ligand complexes. James 2012/2/24 Mark Abraham mark.abra...@anu.edu.au On 24/02/2012 6:31 PM, James Starlight wrote: Up! :) Please provide me with the best sollution of my problem! I just want to copy some water mollecules from X-ray structure to my model and place it in the identical possitions inside the TM budle of my protein. What are the most trivial way to solve this task? You have a non-trivial problem. You can either build the model on the structure that has the waters (pdb2gmx doesn't strip water, IIRC), or work out some geometric criteria for placing the waters afterwards. Not every problem has an existing tool for its solution. Mark James 2012/2/22 James Starlight jmsstarli...@gmail.com Dear Gromacs Users! I want to perform simulation of the membrane receptor in the membtane environment. There are some evidence about precense of the functional-relevant internal water mollecules in the transmembrane alpha-helix bundle of the receptor. I want to take into account that internal water in my model. I have coordinates of the X-ray structures wich have all that water. Also I have perfect model of the same protein wich have not that water but have full-length structure ( there are some missing residues in the X-ray structures- e.g in the loop regions). So what the best way to build system would be in my case? 1- Should I use X-ray structure where internal water has already present and build missing loops via model software ? How I could preserve the internal waters in that starting structure when this structure will be processed by pdb2gmx ? 2- Or the best way is to incorporate all waters in the model of my protein ? If this aproach could be better what is the simplest way to transfer exact coordinates of water in that holo model ? ) Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Internal water in the membrane receptor
On 24/02/2012 6:55 PM, James Starlight wrote: Mark, what about the next sollution firstly I'll align both of my structures ( x-ray with water and another my model without water) than I'll copy aligned water from first structure to my model in the bottom of the GRO file. than I'll minimise this editted structure to relax side chains of the residues wich are in contact with the new waters Might this aproach be usefull? Commonly I use it to prepare protein-ligand complexes. Might work, but there are lots of steric issues and potential problems. Mark James 2012/2/24 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 24/02/2012 6:31 PM, James Starlight wrote: Up! :) Please provide me with the best sollution of my problem! I just want to copy some water mollecules from X-ray structure to my model and place it in the identical possitions inside the TM budle of my protein. What are the most trivial way to solve this task? You have a non-trivial problem. You can either build the model on the structure that has the waters (pdb2gmx doesn't strip water, IIRC), or work out some geometric criteria for placing the waters afterwards. Not every problem has an existing tool for its solution. Mark James 2012/2/22 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com Dear Gromacs Users! I want to perform simulation of the membrane receptor in the membtane environment. There are some evidence about precense of the functional-relevant internal water mollecules in the transmembrane alpha-helix bundle of the receptor. I want to take into account that internal water in my model. I have coordinates of the X-ray structures wich have all that water. Also I have perfect model of the same protein wich have not that water but have full-length structure ( there are some missing residues in the X-ray structures- e.g in the loop regions). So what the best way to build system would be in my case? 1- Should I use X-ray structure where internal water has already present and build missing loops via model software ? How I could preserve the internal waters in that starting structure when this structure will be processed by pdb2gmx ? 2- Or the best way is to incorporate all waters in the model of my protein ? If this aproach could be better what is the simplest way to transfer exact coordinates of water in that holo model ? ) Thanks for help James -- gmx-users mailing list gmx-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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
