[gmx-users] orientation of CNT
Dear gmx users I would like to simulate a system: carbon nanotube+some small molecules. first I want to align CNT along the z direction. to do that I used the commands: editconf -f cnt.pdb -o cnt.gro -princ -box 5 5 5 editconf -f cnt.gro -o nano.gro -rotate 0 90 0 and then I used genbox: genbox -cp nano.gro -ci smallmolecule.pdb -nmol 24 -o out.gro but when I looked at the out.gro in VMD I saw that the orientation of my carbon nanotube has changed slightly.would you please tell me how I can fix that? Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] CHARMM36 - Smaller Area per lipid for POPE - Why?
Hello, I ran into similar issues for a DPPC bilayer. It might be possible that the two leaflets of the bilayer are moving with respect to eachother. If this is not taken into account, these artificial velocities will mean the simulation thinks it is at a higher temperature than it really is. If possible, you might want to try subtracting the center of mass motion of each leaflet, rather than the center of mass motion of the entire bilayer. This will allow the system to equillibrate to the correct (higher) temperature, and should increase the area per lipid of the bilayer. Hope this helps. -David On Thu, Aug 2, 2012 at 8:22 AM, Sebastien Cote wrote: > > > Dear Gromacs users, > > I did new tests on the POPE membrane with CHARMM36 parameters, but I still > always get area per lipid values that are smaller than experimental value by > 4 to 6 Angstrom2. Here are my new tests. > > My initial configuration is an equilibrated POPE membrane with 80 lipids at 1 > atm and 310K in NPT. It was taken from Klauda's website and it was obtained > from the study in which the POPE parameters were tested (Klauda, J. B. et al. > 2010 J. Phys. Chem. B, 114, 7830-7843). > > I use TIPS3P (Charmm's special TIP3P). My simulations parameters are similar > to those used in a previous tread on the Gromacs mailing list > (http://lists.gromacs.org/pipermail/gmx-users/2010-October/055161.html for > DMPC, POPC and DPPC of 128 lipids each) : > > dt = 0.002 ps; rlist = 1.0 nm; rlistlong = 1.4 nm; coulombtype = pme; > rcoulomb = 1.4 nm; vdwtype = switch or cutoff (see below); DispCorr = No; > fourierspacing = 0.15 nm; pme_order = 6; tcoupl = nose-hoover; tau_t = 1.0 > ps; ref_t = 310K; pcoupl = Parrinello-Rahman; pcoupltype = semiisotropic; > tau_p = 5.0 ps; compressibility = 4.5e-5; ref_p = 1.0 atm; constraints = > h-bonds; constraint_algorithm = LINCS. Nochargegrps was used when executing > pdb2gmx. > > The simulation time of each simulation is 100 ns. I tried different VdW > cutoff values, since it was previously mentioned that cutoff values for VdW > may influence the area per lipid. The average value and standard deviation > are calculated on the 20 to 100 ns time interval. > > 1- For VdW switch from 0.8 to 1.2 nm : The area per lipid is 54.8 +/- 1.6 A2. > 2- For VdW switch from 1.1 to 1.2 nm : The area per lipid is 54.6 +/- 1.8 A2. > 3- For VdW cutoff at 1.4 nm : The area per lipid is 55.9 +/- 1.6 A2. > > I also checked the influence of DispCorr with VdW switch from 0.8 to 1.2 nm : > > 1- Without DispCorr : The area per lipid is 54.8 +/- 1.6 A2. > 2- With DispCorr :The area per lipid is 54.4 +/- 1.9 A2. > > I also checked the influence of PME cutoff with VdW switch from 0.8 to 1.2 nm > : > > 1- For PME cutoff at 1.4 nm : The area per lipid is 54.8 +/- 1.6 A2. > 2- For PME cutoff at 1.0 nm : The area per lipid is 56.4 +/- 1.5 A2. > > These values are smaller than 4-6 A2 when compared against the experimental > value (59.75-60.75 A2) and the value obtained in Klauda's simulation (59.2 > +/- 0.3 A2). DispCorr and LJ cutoff weakly impact the results. Reducing the > PME cutoff seems to have the greatest effect, but the value obtained is still > smaller than experimental value by 3-4 A2. > > I also tried other initial configurations, but the results were either very > similar or worst. > > Larger membrane gave similar results for the mean values and smaller standard > deviations. > > --- > > Have anyone else tried to simulate a CHARMM36 POPE membrane in Gromacs? Do > you get similar results? > > Is a 3-4 A2 deviation from experiment likely to influence my membrane/peptide > simulations? Would it then be preferable to go with CHARMM27 in the NPAT > ensemble? > > At this point, I have no clue of how to reproduce correctly Klauda's results > for POPE. Any suggestion is welcomed. > > Thanks, > > Sebastien > > > > > Date: Mon, 23 Jul 2012 16:06:40 -0500 > > From: p...@uab.edu > > To: gmx-users@gromacs.org > > Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why? > > > > On 2012-07-23 02:34:31PM -0300, Sebastien Cote wrote: > > > > > > There is not much difference when using DispCorr or not. At least on the > > > same time scale as the simulation with switch cutoff from 0.8 to 1.2 nm > > > and on the same time scale. > > > > > > Should DispCorr be used in all membrane simulations? I thought that we > > > should always use this correction. > > > > I alwasy thought it was actually forcefield dependent. I never use it with > > CHARMM since the mdp files I used as the basis for mine didn't with C27, and > > I get acceptable APL with POPC when using the same mdp with C36. I haven't > > compared the codes for CHARMM to see if dispcorr is builtin to the gromacs > > implementation or not, but the reason I brought it up is that on past > > mailing list discussions about TIPS3P, there were reports of significant > > density differences with and
Re: [gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
On 8/3/12 11:01 AM, bhavaniprasad vipperla wrote: Hi I tried to run the minimization step . Minimization went on well but am not confout.gro Is there any specific command for obtaining an confout.gro while running em. If mdrun did not write an output .gro file, then it did not complete. Check the log file; the run probably crashed. Note that if you have used the -deffnm flag, the name of the file is not going to be confout.gro but will be whatever you've defined. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
Hi I tried to run the minimization step . Minimization went on well but am not confout.gro Is there any specific command for obtaining an confout.gro while running em. Regards -Original Message- From: Justin Lemkul Sent: 3 Aug 2012 14:55:25 GMT To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology On 8/3/12 10:52 AM, bhavaniprasad vipperla wrote: > Hi Justin > Could u suggest me which step to carry on further. > It's not clear to me that InflateGRO truly failed, though some of the output is curious, as noted before. > In place of inflategro , can we use g_membed. > Sure. I don't use it personally, but others do. -Justin > Regards > Bhavaniprasad > > -Original Message- > > From: Justin Lemkul > Sent: 3 Aug 2012 10:54:49 GMT > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Re: number of coordinates in coordinate file > (system_inflated.gro, 9331) number of coordinates in coordinate file does > not match topology > > > > On 8/3/12 12:32 AM, Bhavaniprasad.V wrote: >> hi justin, >> >> the problem is actually InflateGro is not deleting any lipids. >> I had inserted the protein in lipid using VMD and saved the coordinate file >> and >> using that directly to this step >> >> cat pro_in_pope.gro pope_whole.gro > system.gro >> >> after running perl inflategro.pl system.gro 4 POPE 14 system_inflated.gro 5 >> area.dat. >> Argument "P8" isn't numeric in printf at inflategro.pl line 708. >> Argument "O9" isn't numeric in printf at inflategro.pl line 708. >> >> Calculating Area per lipid... >> Protein X-min/max: -4103 >> Protein Y-min/max: -14100 >> X-range: 107 AY-range: 114 A >> Building 107 X 114 2D grid on protein coordinates... >> Calculating area occupied by protein.. >> full TMD.. >> upper TMD >> lower TMD >> Area per protein: 107.75 nm^2 >> Area per lipid: 8.02906194817911 nm^2 >> >> Area per protein, upper half: 101.25 nm^2 >> Area per lipid, upper leaflet : 8.09202321149701 nm^2 >> >> Area per protein, lower half: 102.25 nm^2 >> Area per lipid, lower leaflet : 8.03790402571429 nm^2 >> >> Writing Area per lipid... >> Done! >> >> So please suggest me what is going wrong >> > > The errors above indicate something is going wrong with printing the output, > but > from looking at the code I see no reason why this should come up. It is also > quite possible that no lipids need to be deleted based on the inflated > structure. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 > -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Protein from the line chain
On Fri, Aug 3, 2012 at 3:51 PM, Justin Lemkul wrote: > > > On 8/3/12 10:47 AM, Steven Neumann wrote: >> >> On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul wrote: >>> >>> >>> >>> On 8/3/12 10:27 AM, Steven Neumann wrote: Dear Gmx Users, I want to simulate protein line chain (80 residues) in explicit sovent. Let's assume its axis is x direction. What should be the z and y dimension of the box? Is there any rule? Would you wait e.g. for 50 >>> >>> >>> >>> The box size in all dimensions needs to be sufficient to accommodate the >>> protein chain in a fully extended configuration aligned with any axis. >>> You >>> can't predict how the protein will rotate, and it is possible (though >>> probably unlikely) to rotate 90 degrees in any direction without >>> collapsing >>> at all. A dodecahedral box is your friend here, but a huge amount of >>> atoms >>> is unavoidable. >>> >>> ns when it folds and then decrease the simulation box? >>> >>> In doing so, you have to justify your results in the context of a >>> discontinuous series of simulations. Implicit solvent may be a much more >>> advantageous approach. >>> >>> -Justin >> >> >> >> Thank you. What do you mean by discontinuous series of simulations? I >> have to use explicit solvent unfortunately. Once it folds in a huge >> box I can stop it and place it into the smaller one. >> > > Precisely - you run one simulation, obtain a configuration (is it > representative of the first part of the simulation? randomly chosen?) and > re-solvate it such that hydration is disrupted unless you take care to > extract a solvation shell around the protein. Even then, you can't preserve > the previous state with respect to thermodynamic observables so it's > basically a new simulation from some arbitrarily chosen configuration. If > you're studying protein folding, that can seem a bit fishy. In principle, > there's nothing immediately wrong with doing this, but always be prepared to > justify your approach. There are a lot of very tricky questions a reviewer > can ask if care is not taken. > > -Justin > Thank you Justin for the clear explanation. Steven > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
On 8/3/12 10:52 AM, bhavaniprasad vipperla wrote: Hi Justin Could u suggest me which step to carry on further. It's not clear to me that InflateGRO truly failed, though some of the output is curious, as noted before. In place of inflategro , can we use g_membed. Sure. I don't use it personally, but others do. -Justin Regards Bhavaniprasad -Original Message- From: Justin Lemkul Sent: 3 Aug 2012 10:54:49 GMT To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology On 8/3/12 12:32 AM, Bhavaniprasad.V wrote: hi justin, the problem is actually InflateGro is not deleting any lipids. I had inserted the protein in lipid using VMD and saved the coordinate file and using that directly to this step cat pro_in_pope.gro pope_whole.gro > system.gro after running perl inflategro.pl system.gro 4 POPE 14 system_inflated.gro 5 area.dat. Argument "P8" isn't numeric in printf at inflategro.pl line 708. Argument "O9" isn't numeric in printf at inflategro.pl line 708. Calculating Area per lipid... Protein X-min/max: -4103 Protein Y-min/max: -14100 X-range: 107 AY-range: 114 A Building 107 X 114 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 107.75 nm^2 Area per lipid: 8.02906194817911 nm^2 Area per protein, upper half: 101.25 nm^2 Area per lipid, upper leaflet : 8.09202321149701 nm^2 Area per protein, lower half: 102.25 nm^2 Area per lipid, lower leaflet : 8.03790402571429 nm^2 Writing Area per lipid... Done! So please suggest me what is going wrong The errors above indicate something is going wrong with printing the output, but from looking at the code I see no reason why this should come up. It is also quite possible that no lipids need to be deleted based on the inflated structure. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
Hi Justin Could u suggest me which step to carry on further. In place of inflategro , can we use g_membed. Regards Bhavaniprasad -Original Message- From: Justin Lemkul Sent: 3 Aug 2012 10:54:49 GMT To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology On 8/3/12 12:32 AM, Bhavaniprasad.V wrote: > hi justin, > > the problem is actually InflateGro is not deleting any lipids. > I had inserted the protein in lipid using VMD and saved the coordinate file > and > using that directly to this step > > cat pro_in_pope.gro pope_whole.gro > system.gro > > after running perl inflategro.pl system.gro 4 POPE 14 system_inflated.gro 5 > area.dat. > Argument "P8" isn't numeric in printf at inflategro.pl line 708. > Argument "O9" isn't numeric in printf at inflategro.pl line 708. > > Calculating Area per lipid... > Protein X-min/max: -4103 > Protein Y-min/max: -14100 > X-range: 107 AY-range: 114 A > Building 107 X 114 2D grid on protein coordinates... > Calculating area occupied by protein.. > full TMD.. > upper TMD > lower TMD > Area per protein: 107.75 nm^2 > Area per lipid: 8.02906194817911 nm^2 > > Area per protein, upper half: 101.25 nm^2 > Area per lipid, upper leaflet : 8.09202321149701 nm^2 > > Area per protein, lower half: 102.25 nm^2 > Area per lipid, lower leaflet : 8.03790402571429 nm^2 > > Writing Area per lipid... > Done! > > So please suggest me what is going wrong > The errors above indicate something is going wrong with printing the output, but from looking at the code I see no reason why this should come up. It is also quite possible that no lipids need to be deleted based on the inflated structure. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Protein from the line chain
On 8/3/12 10:47 AM, Steven Neumann wrote: On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul wrote: On 8/3/12 10:27 AM, Steven Neumann wrote: Dear Gmx Users, I want to simulate protein line chain (80 residues) in explicit sovent. Let's assume its axis is x direction. What should be the z and y dimension of the box? Is there any rule? Would you wait e.g. for 50 The box size in all dimensions needs to be sufficient to accommodate the protein chain in a fully extended configuration aligned with any axis. You can't predict how the protein will rotate, and it is possible (though probably unlikely) to rotate 90 degrees in any direction without collapsing at all. A dodecahedral box is your friend here, but a huge amount of atoms is unavoidable. ns when it folds and then decrease the simulation box? In doing so, you have to justify your results in the context of a discontinuous series of simulations. Implicit solvent may be a much more advantageous approach. -Justin Thank you. What do you mean by discontinuous series of simulations? I have to use explicit solvent unfortunately. Once it folds in a huge box I can stop it and place it into the smaller one. Precisely - you run one simulation, obtain a configuration (is it representative of the first part of the simulation? randomly chosen?) and re-solvate it such that hydration is disrupted unless you take care to extract a solvation shell around the protein. Even then, you can't preserve the previous state with respect to thermodynamic observables so it's basically a new simulation from some arbitrarily chosen configuration. If you're studying protein folding, that can seem a bit fishy. In principle, there's nothing immediately wrong with doing this, but always be prepared to justify your approach. There are a lot of very tricky questions a reviewer can ask if care is not taken. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein from the line chain
On Fri, Aug 3, 2012 at 3:34 PM, Justin Lemkul wrote: > > > On 8/3/12 10:27 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I want to simulate protein line chain (80 residues) in explicit >> sovent. Let's assume its axis is x direction. What should be the z and >> y dimension of the box? Is there any rule? Would you wait e.g. for 50 > > > The box size in all dimensions needs to be sufficient to accommodate the > protein chain in a fully extended configuration aligned with any axis. You > can't predict how the protein will rotate, and it is possible (though > probably unlikely) to rotate 90 degrees in any direction without collapsing > at all. A dodecahedral box is your friend here, but a huge amount of atoms > is unavoidable. > > >> ns when it folds and then decrease the simulation box? >> > > In doing so, you have to justify your results in the context of a > discontinuous series of simulations. Implicit solvent may be a much more > advantageous approach. > > -Justin Thank you. What do you mean by discontinuous series of simulations? I have to use explicit solvent unfortunately. Once it folds in a huge box I can stop it and place it into the smaller one. Steven > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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] Protein from the line chain
On 8/3/12 10:27 AM, Steven Neumann wrote: Dear Gmx Users, I want to simulate protein line chain (80 residues) in explicit sovent. Let's assume its axis is x direction. What should be the z and y dimension of the box? Is there any rule? Would you wait e.g. for 50 The box size in all dimensions needs to be sufficient to accommodate the protein chain in a fully extended configuration aligned with any axis. You can't predict how the protein will rotate, and it is possible (though probably unlikely) to rotate 90 degrees in any direction without collapsing at all. A dodecahedral box is your friend here, but a huge amount of atoms is unavoidable. ns when it folds and then decrease the simulation box? In doing so, you have to justify your results in the context of a discontinuous series of simulations. Implicit solvent may be a much more advantageous approach. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Protein from the line chain
Dear Gmx Users, I want to simulate protein line chain (80 residues) in explicit sovent. Let's assume its axis is x direction. What should be the z and y dimension of the box? Is there any rule? Would you wait e.g. for 50 ns when it folds and then decrease the simulation box? thank you Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] LIE using g_lie
Dear colleagues, I have some doubts about LIE and would like some clarifications. While I calculate the LIE using g_lie, it gives the DGbind energy in KJ/mol and a standard deviation in parentheses. How well can I use this value alone or meaningful it is by itself in comparing the binding affinity of a set of ligands (not calculating the same for the ligand-only system) ? Another query is that, to calculate the DGbind using the following formula DGbind = vdw_bound - vdw_free + Elec_bound - Elec_free Are the values calculated by -Clj tag is the value for vdw_bound or vdw_free and -Cqq is for Elec_bound or Elec_free? In another literature, this formula is further detailed DGbind_formula http://gromacs.5086.n6.nabble.com/file/n444/DGbind.jpg where alpha, beta and gamma values are also needed, what are these values and how to calculate them? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/LIE-using-g-lie-tp444.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Thole polarization between different molecules
On 2012-08-02 16:01, avilaverde wrote: Hi, I'm interested in using models that require Thole polarization in Gromacs but I'm having trouble understanding the syntax of the [thole_polarization] entry because it is not yet explained in the manual. I've looked online for examples but could not find any that applied to the case I am interested in. Can someone send me an example file where this parameter is used in a simulation containing more than one type of molecule (e.g. water and Mg2+)? This is not possible in the current code. I found one example on the Gromacs lists (http://lists.gromacs.org/pipermail/gmx-developers/2006-March/001571.html) : ;[ thole_polarization ] ;dipole 1dipole 2 ;at1 at2at1 at2func const pol dip 1 pol dip 2 1 5 6 9 2 2.6 0.001237576 0.001217571 The problem is that in this example I can only specify Thole polarization-type interactions between atoms belonging to the same molecule because these interactions are described by atom id, not atom type (I tried using atom types, without success). Can anyone point me in the right direction? Thank you, Ana -- View this message in context: http://gromacs.5086.n6.nabble.com/Thole-polarization-between-different-molecules-tp428.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] place carbon nanotube along the z direction
You can use editconf -princ to orient it into the principal axis. Then with editconf -rotate specify proper vector of 90 degrees if required. Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Abed Askari [abedask...@yahoo.com] Sent: Friday, August 03, 2012 1:06 PM To: gmx-users@gromacs.org Subject: [gmx-users] place carbon nanotube along the z direction Dear gmx-users I would like to orient my carbon nanotube along the z direction. would you please tell me how I can do that?Do I use any option other than -box when I use editconf or something?my command was editconf -f cnt.pdb -o cnt.gro -box 5 5 5 any help would be really appreciated. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] place carbon nanotube along the z direction
Dear gmx-users I would like to orient my carbon nanotube along the z direction. would you please tell me how I can do that?Do I use any option other than -box when I use editconf or something?my command was editconf -f cnt.pdb -o cnt.gro -box 5 5 5 any help would be really appreciated. Best regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology
On 8/3/12 12:32 AM, Bhavaniprasad.V wrote: hi justin, the problem is actually InflateGro is not deleting any lipids. I had inserted the protein in lipid using VMD and saved the coordinate file and using that directly to this step cat pro_in_pope.gro pope_whole.gro > system.gro after running perl inflategro.pl system.gro 4 POPE 14 system_inflated.gro 5 area.dat. Argument "P8" isn't numeric in printf at inflategro.pl line 708. Argument "O9" isn't numeric in printf at inflategro.pl line 708. Calculating Area per lipid... Protein X-min/max: -4103 Protein Y-min/max: -14100 X-range: 107 AY-range: 114 A Building 107 X 114 2D grid on protein coordinates... Calculating area occupied by protein.. full TMD.. upper TMD lower TMD Area per protein: 107.75 nm^2 Area per lipid: 8.02906194817911 nm^2 Area per protein, upper half: 101.25 nm^2 Area per lipid, upper leaflet : 8.09202321149701 nm^2 Area per protein, lower half: 102.25 nm^2 Area per lipid, lower leaflet : 8.03790402571429 nm^2 Writing Area per lipid... Done! So please suggest me what is going wrong The errors above indicate something is going wrong with printing the output, but from looking at the code I see no reason why this should come up. It is also quite possible that no lipids need to be deleted based on the inflated structure. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
