Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers
Hi James, You could also have look at our website: http://people.su.se/~jjm There you find a number of bilayers ready to use (among them there is a POPE bilayer). They were generated with another FF but if you wish to use CHARMM you can since the atom numbering/naming is the same for Slipids and CHARMM. Best, Joakim Message: 2 Date: Tue, 18 Dec 2012 21:07:22 -0800 From: James Starlight jmsstarli...@gmail.com Subject: Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAALQopzb3eS5DCL7vKN+S3e7BBLADxo6ETDg2t8BD1=jy7x...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Justin, thanks again. As I understood gromacs already had had parameters for charmm lipid so the main approach is to do ITP file for 1 lipid by means of pdb2gmx isnt it? By the way is there any way to convert PSF or CRD file to PDB? I've found suitable bilayer for my simulation but it lack such coordinates. POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs): CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD 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] time-dependent electric field
Dear Gromacs users, I would like to simulate a protein with pulsed, time-dependent electric field (similiarly to Picosecond melting of ice... article). After taking a look on the mailing list archive, I have set the the E_* parameters according to the manual. Also made some test runs, and checked field.xvg (nice oscillating field but this is not what I really need). I have checked the source (sim_util.c) also, and found the code for time-dependent field, so my question is, where can I set the wavelength, the width, and the t_0 value of the laser pulse in the mdp file? My E_x parameters were: 1 0.03 1 Also tried E_xt (according to http://gromacs.5086.n6.nabble.com/Oscillating-Electrical-Field-tt4430547.html), but no succes. I would appreciate any help, best regards: Norbert Jeszenői -- 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] Where to stop with TM protein PMF calculations
Good morning, A bit of a long one I am afraid. I am simulating a transmembrane dimer, and calculating the association free energy through potential of mean force calculations as a function of interhelical distance. I have got very good umbrella coverage along my reaction coordinate, however, I would like to know where I should stop calculating and normalise to zero? I am comparing two systems of identical composition but with a different conformation. Hence, the normalising step is vital. Looking in the literature the cut offs used seem to be around 2nm (two JACS papers come to mind). I've pulled as far as needed to reach a plateau in the PMF curve. This is around 6.5 nm to 8 nm. The problem is if I normalise at the plateau (which seems to be the beliefs of the professors at my institute), the comparative free energy between the two systems is very different to normalising at 2nm (note: the papers in literature do not observe a plateau, there is still an obvious upward trend at their cutoff). I need justification of where to normalise. According to literature they cut off outside of interaction range. I have decided to test umbrella windows along the reaction coordinate by decomposing the energy of the system. LJ short and Coul short between peptides at a reaction coordinate distance of 8 nm, is 0 as expected. However, I am still getting energy values on Coul. recip even when I decompose (although the gromacs literature says I can't) the system by systematically setting every charge to zero, i.e., Peptide A (A), Peptide B (B), SOL, lipid and counter ions have zero charge throughout. E_coul_recip_A_B = E_coul_recip_(A_B,A_A,B_B) - (E_coul_recip_A_A + E_coul_recip_B_B) All charges are zero, with the exception to peptide A in E_coul_recip_A_A and peptide B in E_coul_recip_B_B. and peptide A and B in E_coul_recip_(A_B,A_A,B_B). When I add E_coul_recip_A_B to the LJ short and Coul short I do not get an energy of zero. So: 1) The coul-recip decomposition, is this a flawed approach? The gromacs manual says it can't be decomposed. 2) Where along the reaction coordinate should I cut off? 3) Why don't authors pull until they reach a plateau? Many many thanks Anthony -- 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] PME vs Shift: Cut offs
Hello all, I am trying to compare PME and shift electrostatics methods for my hydrocarbon system. In both cases rlist = 1.35 , but in case of PME rcoulomb= 1.35 while for shift ** rcoulomb= 1.1. I see no significant change (less than 1%) in total system potential, however I would like to know if I can also conclude that electrostatic energy is insensitive to rcoulomb as a result of change from 1.1 (shift) to 1.35 (PME). * * ** Is this a correct interpretation? Thank you for your help, * * *CASE 1:* *coulombtype = PME* vdw-type = Shift ; Cut-offs rlist = 1.35 *rcoulomb= 1.35 * rvdw= 1.1 rcoulomb-switch = 1 rvdw-switch = 1 * * *CASE 2:* *coulombtype = Shift * vdw-type = Shift ; Cut-offs rlist = 1.35 *rcoulomb= 1.1* rvdw= 1.1 rcoulomb-switch = 1 rvdw-switch = 1 -- Thanks, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] Mutation-induced binding affinity change using BAR
Hi Gromacs People, we want to do a BAR calculation to calculate the binding affinity change induced by a mutation. That means: - We want to transform a residue from aminoacid1 (aa1) to aminoacid2 (aa2) in a single-transformation approach (transforming both vdw and coulomb at the same time) lambda=0 : aa1 switched on and aa2 switched off lambda=1 : aa1 switched off and aa2 switched on - to calculate binding free energy, we would calculate this transformation process once in the complex and once in the receptor and calculate the difference However, I can find no information how to have both aminoacids switched on half, for example for lambda=0.5 Any tutorials I found decouple atoms from its environment but not with switching on different atoms at the same time. In Amber, this is possible by using two topologies. Is this possible with Gromacs and where can I read how to do it? A simpler example illustration the problem would be: Transforming Toluene (Benzol-CH3) to Phenole (Benzol-OH) in water (to calculate the change in solvation energy) from lambda 0 to 1, -CH3 interactions should be gradually switched off and -OH switched on (with both switched on half at lambda=0.5) For further disambiguition: We want to perform equilibrium simulations at discrete lambda steps (with delta_lambda=0 for each simulation) - no slow growth Any help is greatly appreciated. Greets Oliver -- 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: gmx-users Digest, Vol 104, Issue 83
Dear Justin I want exactly this, that the distance between Au-S be stable around equilibrium value, For this purpose,Should I put the harmonic parameters related to the gold and sulfur in ffbonded file? Or I should consider AU-S connection as VonderWaals and put its epsilon and sidma in ffnonbonded file? thank you Fatemeh Ramezani From: gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org To: gmx-users@gromacs.org Sent: Tuesday, 18 December 2012, 14:30 Subject: gmx-users Digest, Vol 104, Issue 83 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. merge .gro, .top files (Kieu Thu Nguyen) 2. Re: GPU running problem with GMX-4.6 beta2 (Albert) 3. Re: merge .gro, .top files (Tsjerk Wassenaar) 4. Re: merge .gro, .top files (Erik Marklund) 5. Re: merge .gro, .top files (Vedat Durmaz) 6. Re: Re: gold-S simulation (francesco oteri) -- Message: 1 Date: Tue, 18 Dec 2012 12:18:38 +0700 From: Kieu Thu Nguyen kieuthu2...@gmail.com Subject: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CACrJSRgRHUbjqW+Zpfq=yfmcuh9ow68d2kmvklghez3acas...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- Message: 2 Date: Tue, 18 Dec 2012 09:20:05 +0100 From: Albert mailmd2...@gmail.com Subject: Re: [gmx-users] GPU running problem with GMX-4.6 beta2 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 50d02735.9030...@gmail.com Content-Type: text/plain; charset=UTF-8; format=flowed On 12/17/2012 08:06 PM, Justin Lemkul wrote: It seems to me that the system is simply crashing like any other that becomes unstable. Does the simulation run at all on plain CPU? -Justin Thank you very much Justin, it's really helpful. I've checked that the structure after minization and found that there is some problem with my ligand. I regenerated the ligand toplogy with acpype, and resubmit for mimization and NVT. Now it goes well. So probably the problems comes from the incorrect ligand topolgy which make the system very unstable. best Albert -- Message: 3 Date: Tue, 18 Dec 2012 09:30:04 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: cabze1siujhgv4o8ndjfsnu4pxtketqmhxdi2i77vhp60nnj...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi KT, If you mean concatenating frames in .gro files, you can use trjcat or just cat. If you mean merging the coordinates, it's a wee bit more complicated. Since you also ask for top files, I guess that's the case. Here's a snippet of python code that will do the trick: #!/usr/bin/env python import sys f = [open(i).readlines() for i in sys.argv[1:]] print Merged gro file\n%5d % (sum([len(i) for i in f]) - 3*len(f)) print .join([.join(i[2:-1]) for i in f]), print f[0][-1] For the top files, it is necessary to ensure all the moleculetypes are #included, and that the [ molecules ] listing under [ system ] has the right number and order of the molecules in the merged gro file. There's no tool for that that I know of. Cheers, Tsjerk On Tue, Dec 18, 2012 at 6:18 AM, Kieu Thu Nguyen kieuthu2...@gmail.comwrote: Dear All, I don't know which tools used to merge 2 files .gro, 2 files .top ? Can i use trjcat ? Thanks ! KT -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- Message: 4 Date: Tue, 18 Dec 2012 09:38:41 +0100 From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] merge .gro, .top files To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: bd5228d7-229f-4e9c-9f03-66836dd50...@xray.bmc.uu.se Content-Type: text/plain; charset=us-ascii 18 dec 2012 kl. 09.30 skrev
Re: [gmx-users] gold-S simulation
On 12/19/12 6:02 AM, fatemeh ramezani wrote: Dear Justin I want exactly this, that the distance between Au-S be stable around equilibrium value, For this purpose,Should I put the harmonic parameters related to the gold and sulfur in ffbonded file? Or I should consider AU-S connection as VonderWaals and put its epsilon and sidma in ffnonbonded file? Please be mindful to only parse the relevant portion of the digest and to use a real subject line. Yes, if you want there to be a covalent bond, you need to introduce one. Hoping that van der Waals parameters will hold the elements of the system in place does not sound like a robust approach to me. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Mutation-induced binding affinity change using BAR
On 12/19/12 5:29 AM, Oliver Kuhn wrote: Hi Gromacs People, we want to do a BAR calculation to calculate the binding affinity change induced by a mutation. That means: - We want to transform a residue from aminoacid1 (aa1) to aminoacid2 (aa2) in a single-transformation approach (transforming both vdw and coulomb at the same time) lambda=0 : aa1 switched on and aa2 switched off lambda=1 : aa1 switched off and aa2 switched on - to calculate binding free energy, we would calculate this transformation process once in the complex and once in the receptor and calculate the difference However, I can find no information how to have both aminoacids switched on half, for example for lambda=0.5 Any tutorials I found decouple atoms from its environment but not with switching on different atoms at the same time. In Amber, this is possible by using two topologies. Is this possible with Gromacs and where can I read how to do it? The dual topology approach is discussed in manual section 5.7.4. -Justin A simpler example illustration the problem would be: Transforming Toluene (Benzol-CH3) to Phenole (Benzol-OH) in water (to calculate the change in solvation energy) from lambda 0 to 1, -CH3 interactions should be gradually switched off and -OH switched on (with both switched on half at lambda=0.5) For further disambiguition: We want to perform equilibrium simulations at discrete lambda steps (with delta_lambda=0 for each simulation) - no slow growth Any help is greatly appreciated. Greets Oliver -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Where to stop with TM protein PMF calculations
On 12/19/12 4:12 AM, Nash, Anthony wrote: Good morning, A bit of a long one I am afraid. I am simulating a transmembrane dimer, and calculating the association free energy through potential of mean force calculations as a function of interhelical distance. I have got very good umbrella coverage along my reaction coordinate, however, I would like to know where I should stop calculating and normalise to zero? I am comparing two systems of identical composition but with a different conformation. Hence, the normalising step is vital. Looking in the literature the cut offs used seem to be around 2nm (two JACS papers come to mind). I've pulled as far as needed to reach a plateau in the PMF curve. This is around 6.5 nm to 8 nm. The problem is if I normalise at the plateau (which seems to be the beliefs of the professors at my institute), the comparative free energy between the two systems is very different to normalising at 2nm (note: the papers in literature do not observe a plateau, there is still an obvious upward trend at their cutoff). I need justification of where to normalise. According to literature they cut off outside of interaction range. I have decided to test umbrella windows along the reaction coordinate by decomposing the energy of the system. LJ short and Coul short between peptides at a reaction coordinate distance of 8 nm, is 0 as expected. However, I am still getting energy values on Coul. recip even when I decompose (although the gromacs literature says I can't) the system by systematically setting every charge to zero, i.e., Peptide A (A), Peptide B (B), SOL, lipid and counter ions have zero charge throughout. E_coul_recip_A_B = E_coul_recip_(A_B,A_A,B_B) - (E_coul_recip_A_A + E_coul_recip_B_B) All charges are zero, with the exception to peptide A in E_coul_recip_A_A and peptide B in E_coul_recip_B_B. and peptide A and B in E_coul_recip_(A_B,A_A,B_B). When I add E_coul_recip_A_B to the LJ short and Coul short I do not get an energy of zero. So: 1) The coul-recip decomposition, is this a flawed approach? The gromacs manual says it can't be decomposed. It's not trivial to do. There are some posts about really detailed ways that you might pull it off, but I don't know whether it's worth the effort. If the umbrella sampling simulations were conducted with PME, there is never a true non-interacting state. There is always some finite contribution to long-range electrostatics terms. 2) Where along the reaction coordinate should I cut off? I would believe the longer distance. At 2 nm, you still may have induced order in either lipids or water between your two proteins, thus affecting the forces between them. I see no reason to think that if a plateau has not been established that the results should be correct. It could be argued that all you're doing is picking some random point along the reaction coordinate and calling it dissociated for the sake of convenience. 3) Why don't authors pull until they reach a plateau? I have seen several published papers that appear to have very arbitrary stopping points, so just because it's published, doesn't mean it's perfect :) I believe in a plateau, a demonstration that, within the caveats inherent to the system, the interactions between the two molecules of interest are insignificant. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Where to stop with TM protein PMF calculations
Hi Justin, Thanks for the swift reply. I am now convinced that the 'plateau' approach is the best. This brings me to a further concern. Take two systems (umbrella sampling along a reaction coordinate etc..) which are identical in composition, yet different in conformation e.g., a helical tilt/crossing angle. I run the two systems along a reaction coordinate until I have a plateau. Both systems exhibit a plateau at around 6.5 - 7.5 nm. However, there is a significant difference in free energy (as a theoretical example 50 kj mol^-1 difference) at this region, which would bias the difference in free energy when I normalise both graphs to zero at this point. Given that both systems are atomistically identical, one would assume an identical free energy when the helices are far enough apart that they don't interact. By using g_wham in increments of 1 ns (0-1 ns, 0-2 ns, 0-3 ns,.), I can see how the curve near the interfacing helices converges, yet at 4+ nm the curve is still dropping. Would you advice that I run additional windows near the plateau region so it is identical in value across both systems? Many thanks Anthony From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 19 December 2012 13:23 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Where to stop with TM protein PMF calculations On 12/19/12 4:12 AM, Nash, Anthony wrote: Good morning, A bit of a long one I am afraid. I am simulating a transmembrane dimer, and calculating the association free energy through potential of mean force calculations as a function of interhelical distance. I have got very good umbrella coverage along my reaction coordinate, however, I would like to know where I should stop calculating and normalise to zero? I am comparing two systems of identical composition but with a different conformation. Hence, the normalising step is vital. Looking in the literature the cut offs used seem to be around 2nm (two JACS papers come to mind). I've pulled as far as needed to reach a plateau in the PMF curve. This is around 6.5 nm to 8 nm. The problem is if I normalise at the plateau (which seems to be the beliefs of the professors at my institute), the comparative free energy between the two systems is very different to normalising at 2nm (note: the papers in literature do not observe a plateau, there is still an obvious upward trend at their cutoff). I need justification of where to normalise. According to literature they cut off outside of interaction range. I have decided to test umbrella windows along the reaction coordinate by decomposing the energy of the system. LJ short and Coul short between peptides at a reaction coordinate distance of 8 nm, is 0 as expected. However, I am still getting energy values on Coul. recip even when I decompose (although the gromacs literature says I can't) the system by systematically setting every charge to zero, i.e., Peptide A (A), Peptide B (B), SOL, lipid and counter ions have zero charge throughout. E_coul_recip_A_B = E_coul_recip_(A_B,A_A,B_B) - (E_coul_recip_A_A + E_coul_recip_B_B) All charges are zero, with the exception to peptide A in E_coul_recip_A_A and peptide B in E_coul_recip_B_B. and peptide A and B in E_coul_recip_(A_B,A_A,B_B). When I add E_coul_recip_A_B to the LJ short and Coul short I do not get an energy of zero. So: 1) The coul-recip decomposition, is this a flawed approach? The gromacs manual says it can't be decomposed. It's not trivial to do. There are some posts about really detailed ways that you might pull it off, but I don't know whether it's worth the effort. If the umbrella sampling simulations were conducted with PME, there is never a true non-interacting state. There is always some finite contribution to long-range electrostatics terms. 2) Where along the reaction coordinate should I cut off? I would believe the longer distance. At 2 nm, you still may have induced order in either lipids or water between your two proteins, thus affecting the forces between them. I see no reason to think that if a plateau has not been established that the results should be correct. It could be argued that all you're doing is picking some random point along the reaction coordinate and calling it dissociated for the sake of convenience. 3) Why don't authors pull until they reach a plateau? I have seen several published papers that appear to have very arbitrary stopping points, so just because it's published, doesn't mean it's perfect :) I believe in a plateau, a demonstration that, within the caveats inherent to the system, the interactions between the two molecules of interest are insignificant. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu
Re: [gmx-users] Where to stop with TM protein PMF calculations
On 12/19/12 8:39 AM, Nash, Anthony wrote: Hi Justin, Thanks for the swift reply. I am now convinced that the 'plateau' approach is the best. This brings me to a further concern. Take two systems (umbrella sampling along a reaction coordinate etc..) which are identical in composition, yet different in conformation e.g., a helical tilt/crossing angle. I run the two systems along a reaction coordinate until I have a plateau. Both systems exhibit a plateau at around 6.5 - 7.5 nm. However, there is a significant difference in free energy (as a theoretical example 50 kj mol^-1 difference) at this region, which would bias the difference in free energy when I normalise both graphs to zero at this point. Given that both systems are atomistically identical, one would assume an identical free energy when the helices are far enough apart that they don't interact. By using g_wham in increments of 1 ns (0-1 ns, 0-2 ns, 0-3 ns,.), I can see how the curve near the interfacing helices converges, yet at 4+ nm the curve is still dropping. Would you advice that I run additional windows near the plateau region so it is identical in value across both systems? If the curves haven't stabilized, then you have a sampling problem, requiring either more windows or longer time within each window. -Justin Many thanks Anthony From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 19 December 2012 13:23 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Where to stop with TM protein PMF calculations On 12/19/12 4:12 AM, Nash, Anthony wrote: Good morning, A bit of a long one I am afraid. I am simulating a transmembrane dimer, and calculating the association free energy through potential of mean force calculations as a function of interhelical distance. I have got very good umbrella coverage along my reaction coordinate, however, I would like to know where I should stop calculating and normalise to zero? I am comparing two systems of identical composition but with a different conformation. Hence, the normalising step is vital. Looking in the literature the cut offs used seem to be around 2nm (two JACS papers come to mind). I've pulled as far as needed to reach a plateau in the PMF curve. This is around 6.5 nm to 8 nm. The problem is if I normalise at the plateau (which seems to be the beliefs of the professors at my institute), the comparative free energy between the two systems is very different to normalising at 2nm (note: the papers in literature do not observe a plateau, there is still an obvious upward trend at their cutoff). I need justification of where to normalise. According to literature they cut off outside of interaction range. I have decided to test umbrella windows along the reaction coordinate by decomposing the energy of the system. LJ short and Coul short between peptides at a reaction coordinate distance of 8 nm, is 0 as expected. However, I am still getting energy values on Coul. recip even when I decompose (although the gromacs literature says I can't) the system by systematically setting every charge to zero, i.e., Peptide A (A), Peptide B (B), SOL, lipid and counter ions have zero charge throughout. E_coul_recip_A_B = E_coul_recip_(A_B,A_A,B_B) - (E_coul_recip_A_A + E_coul_recip_B_B) All charges are zero, with the exception to peptide A in E_coul_recip_A_A and peptide B in E_coul_recip_B_B. and peptide A and B in E_coul_recip_(A_B,A_A,B_B). When I add E_coul_recip_A_B to the LJ short and Coul short I do not get an energy of zero. So: 1) The coul-recip decomposition, is this a flawed approach? The gromacs manual says it can't be decomposed. It's not trivial to do. There are some posts about really detailed ways that you might pull it off, but I don't know whether it's worth the effort. If the umbrella sampling simulations were conducted with PME, there is never a true non-interacting state. There is always some finite contribution to long-range electrostatics terms. 2) Where along the reaction coordinate should I cut off? I would believe the longer distance. At 2 nm, you still may have induced order in either lipids or water between your two proteins, thus affecting the forces between them. I see no reason to think that if a plateau has not been established that the results should be correct. It could be argued that all you're doing is picking some random point along the reaction coordinate and calling it dissociated for the sake of convenience. 3) Why don't authors pull until they reach a plateau? I have seen several published papers that appear to have very arbitrary stopping points, so just because it's published, doesn't mean it's perfect :) I believe in a plateau, a demonstration that, within the caveats inherent to the system, the interactions between the two molecules of interest are insignificant. -Justin --
Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers
Hi Joakim! MAny thanks for such big collection of the bilayers. Have your simulated different protein embedded in that bilayers ? What force field did you use for parametrisation of the proteins for such simulations ? From the mdp file I noticed relatively big cutoffs for vdw as well as electrostatics ( bigger than in charmm force fields). Would it possible to simulate proteins parametrized by charmm in that lipids ussing charmm parametres for whole system? Thanks again, James 2012/12/19 Joakim Jämbeck jamb...@me.com: Joakim -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond index
On 12/19/12 9:37 AM, Kavyashree M wrote: Dear users, While using g_hbond, does it make any difference if I give option 18 and 1 or 1 and 18? Order does not matter. I wanted to find the hydrogen bonding of a group of residues with the whole protein so I had an index of this group. When I give the option as 18 (index number) and 1 (whole protein), I get several messages Hm. This isn't the first time I found this donor (...,...) But later it does calculates. does this mean that it is double counting those interactions? What is group 18? Be mindful of the g_hbond requirement that the chosen groups must be completely unique or completely overlapping. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond index
Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off. Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. Thank you Kavya On Wed, Dec 19, 2012 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/19/12 9:37 AM, Kavyashree M wrote: Dear users, While using g_hbond, does it make any difference if I give option 18 and 1 or 1 and 18? Order does not matter. I wanted to find the hydrogen bonding of a group of residues with the whole protein so I had an index of this group. When I give the option as 18 (index number) and 1 (whole protein), I get several messages Hm. This isn't the first time I found this donor (...,...) But later it does calculates. does this mean that it is double counting those interactions? What is group 18? Be mindful of the g_hbond requirement that the chosen groups must be completely unique or completely overlapping. -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/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] g_hbond index
On 12/19/12 11:43 AM, Kavyashree M wrote: Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off. Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. You see a difference likely because you are invoking the command incorrectly (with overlapping index groups) and it is affecting the way the donor and acceptor arrays are constructed. The proper method of analysis is to monitor H-bonds within group 18 and then between group 18 and whatever part of the protein that does not overlap with it. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] segmentation fault
Sir, I am doing membrane protein dynamics in lipid bilayer, using oplsaa force field. When I am doing minimization after genion I getting message like this Back Off! I just backed up ions_1.tpr.trr to ./#ions_1.tpr.trr.2# ack Off! I just backed up ions_1.tpr.edr to ./#ions_1.tpr.edr.2# Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=5 Segmentation fault Why this coming?I also tried mdrun -nt 1 -deffnm ions.Is it due to any installation problem?I installed gromacs simply from the Ubuntu software center.I searched in mailing list also. Thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_membed *** glibc detected ***
Dear GMX-Users, I've been using g_membed for a while now, and recently I faced this *** glibc detected *** error for a particular system. Being a memory allocation issue, does anyone know something more about it? Here's the command line: g_membed -f system_02.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -n index.ndx - The mdp file is basically the same I always use; - This happens when I'm trying to insert two monomers from the scratch (using the -pieces flag) or a monomer along an already inserted (and frozen) one; - Inserting only one monomer in the system (in the absence of the other) presents no problems. Thanks, Error: . . . Will remove 2 POPC molecules Will remove 122 SOL molecules Will remove 1 NA molecules Will remove 0 CL molecules Back Off! I just backed up temp.top to ./#temp.top.2# *** glibc detected *** g_membed: malloc(): memory corruption: 0x021aa690 *** === Backtrace: = /lib/libc.so.6(+0x776d6)[0x7f47b99f66d6] /lib/libc.so.6(+0x7b77f)[0x7f47b99fa77f] /lib/libc.so.6(__libc_malloc+0x6e)[0x7f47b99fb5ae] /lib/libc.so.6(+0x685cb)[0x7f47b99e75cb] /home/john/gromacs455/lib/libgmx.so.6(gmx_fexist+0x15)[0x7f47ba62f185] /home/john/gromacs455/lib/libgmx.so.6(make_backup+0x2a)[0x7f47ba62f87a] /home/john/gromacs455/lib/libgmx.so.6(ffopen+0x24d)[0x7f47ba63017d] /home/john/gromacs455/lib/libgmxana.so.6(top_update+0x469)[0x7f47bb4477c9] /home/john/gromacs455/lib/libgmxana.so.6(mdrunner_membed+0x2c15)[0x7f47bb455225] /home/john/gromacs455/lib/libgmxana.so.6(gmx_membed+0x1840)[0x7f47bb456c60] g_membed[0x400679] /lib/libc.so.6(__libc_start_main+0xfe)[0x7f47b999dd8e] g_membed[0x4005a9] === Memory map: 0040-00401000 r-xp 08:01 22416383 /home/john/gromacs455/bin/g_membed 0060-00601000 r--p 08:01 22416383 /home/john/gromacs455/bin/g_membed 00601000-00602000 rw-p 1000 08:01 22416383 /home/john/gromacs455/bin/g_membed 01fd2000-021cc000 rw-p 00:00 0 [heap] 7f47b000-7f47b0021000 rw-p 00:00 0 7f47b0021000-7f47b400 ---p 00:00 0 7f47b699-7f47b6c62000 rw-p 00:00 0 7f47b6c62000-7f47b71ca000 rw-p 00:00 0 7f47b7459000-7f47b79c1000 rw-p 00:00 0 7f47b7aea000-7f47b7dbc000 rw-p 00:00 0 7f47b7dbc000-7f47b7faf000 rw-p 00:00 0 7f47b7faf000-7f47b8874000 rw-p 00:00 0 7f47b88d7000-7f47b8ac3000 rw-p 00:00 0 7f47b8acb000-7f47b8cbe000 rw-p 00:00 0 7f47b8d2f000-7f47b8da9000 rw-p 00:00 0 7f47b8da9000-7f47b8f9c000 rw-p 00:00 0 7f47b9088000-7f47b93a5000 rw-p 00:00 0 7f47b9768000-7f47b977d000 r-xp 08:01 8912975 /lib/libgcc_s.so.1 7f47b977d000-7f47b997c000 ---p 00015000 08:01 8912975 /lib/libgcc_s.so.1 7f47b997c000-7f47b997d000 r--p 00014000 08:01 8912975 /lib/libgcc_s.so.1 7f47b997d000-7f47b997e000 rw-p 00015000 08:01 8912975 /lib/libgcc_s.so.1 7f47b997e000-7f47b997f000 rw-p 00:00 0 7f47b997f000-7f47b9af9000 r-xp 08:01 8912982 /lib/libc-2.12.1.so 7f47b9af9000-7f47b9cf9000 ---p 0017a000 08:01 8912982 /lib/libc-2.12.1.so 7f47b9cf9000-7f47b9cfd000 r--p 0017a000 08:01 8912982 /lib/libc-2.12.1.so 7f47b9cfd000-7f47b9cfe000 rw-p 0017e000 08:01 8912982 /lib/libc-2.12.1.so 7f47b9cfe000-7f47b9d03000 rw-p 00:00 0 7f47b9d03000-7f47b9d1b000 r-xp 08:01 8913146 /lib/libpthread-2.12.1.so 7f47b9d1b000-7f47b9f1a000 ---p 00018000 08:01 8913146 /lib/libpthread-2.12.1.so 7f47b9f1a000-7f47b9f1b000 r--p 00017000 08:01 8913146 /lib/libpthread-2.12.1.so 7f47b9f1b000-7f47b9f1c000 rw-p 00018000 08:01 8913146 /lib/libpthread-2.12.1.so 7f47b9f1c000-7f47b9f2 rw-p 00:00 0 7f47b9f2-7f47b9fa2000 r-xp 08:01 8913136 /lib/libm-2.12.1.so 7f47b9fa2000-7f47ba1a1000 ---p 00082000 08:01 8913136 /lib/libm-2.12.1.so 7f47ba1a1000-7f47ba1a2000 r--p 00081000 08:01 8913136 /lib/libm-2.12.1.so 7f47ba1a2000-7f47ba1a3000 rw-p 00082000 08:01 8913136 /lib/libm-2.12.1.so 7f47ba1a3000-7f47ba1ba000 r-xp 08:01 8913138 /lib/libnsl-2.12.1.so 7f47ba1ba000-7f47ba3b9000 ---p 00017000 08:01 8913138 /lib/libnsl-2.12.1.so 7f47ba3b9000-7f47ba3ba000 r--p 00016000 08:01 8913138 /lib/libnsl-2.12.1.so 7f47ba3ba000-7f47ba3bb000 rw-p 00017000 08:01 8913138 /lib/libnsl-2.12.1.so 7f47ba3bb000-7f47ba3bd000 rw-p 00:00 0 7f47ba3bd000-7f47ba3bf000 r-xp 08:01 8913135 /lib/libdl-2.12.1.so 7f47ba3bf000-7f47ba5bf000 ---p 2000
Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers
We have performed relatively long simulations of a WALP23 peptide embedded in DLPC and DOPC bilayers with different flavors of the Amber FF family. Currently I am working with much bigger protein and see good agreement between the simulations and experiments. You could probably use those bilayers with CHARMM, just make sure you equilibrate a while before just to be safe. Best, Joakim On Dec 19, 2012, at 19:22 , gmx-users-requ...@gromacs.org wrote: Date: Wed, 19 Dec 2012 18:45:33 +0300 From: James Starlight jmsstarli...@gmail.com Subject: Re: [gmx-users] Pre-equilibrated CHARMM lipid bilayers To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAALQopyMeJ=g7lrgj+n2pdseo_fw77xzhr38b4eafjmam06...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Joakim! MAny thanks for such big collection of the bilayers. Have your simulated different protein embedded in that bilayers ? What force field did you use for parametrisation of the proteins for such simulations ? From the mdp file I noticed relatively big cutoffs for vdw as well as electrostatics ( bigger than in charmm force fields). Would it possible to simulate proteins parametrized by charmm in that lipids ussing charmm parametres for whole system? Thanks again, 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] Pre-equilibrated CHARMM lipid bilayers
I am not 100% sure how the differences in c36 will affect the parameters you get from SwissParam. Personally I prefer to use ParamChem (CHARMM's version of Swissprot) to give me ligand parameters using CGenFF atomtypes, since I have CGenFF merged into my Charmm36 forcefield in gromacs. On 2012-12-19 10:37:40AM +0300, James Starlight wrote: Peter, many thanks! Could you tell me is there any differences in atom types between charmm27 and charmm36 ff? I'd like to simulate receptor-ligand complex in that bilayer where ligand molecule would be parametrized by Swiss-param ( make topology for the ligands in charmm27 ff). So because receptor and bilayer will be parametrized in charmm36 I'm not sure about proper working of Swiss's topology with that complex. James 2012/12/19 Peter C. Lai p...@uab.edu: http://cesium.hyperfine.info/~peter/gromacs/popc36/ has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters On 2012-12-18 09:07:22PM -0800, James Starlight wrote: Justin, thanks again. As I understood gromacs already had had parameters for charmm lipid so the main approach is to do ITP file for 1 lipid by means of pdb2gmx isnt it? By the way is there any way to convert PSF or CRD file to PDB? I've found suitable bilayer for my simulation but it lack such coordinates. POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs): CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD James 2012/12/18, Justin Lemkul jalem...@vt.edu: On 12/18/12 2:02 PM, James Starlight wrote: Dear Gromacs Users! I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in charmm27 or charmm36 force field and pre-equilibrated in NPT conditions. I'll bevery thankfull to anybody who provide me with the coordinates as well as itp file for such bilayer. http://terpconnect.umd.edu/~jbklauda/research/download.html Google is your friend. There are plenty more places to look. A search for POPC CHARMM membrane coordinates (without the quotes) does the trick. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 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] increase of temperature or pressure
Dear users, When analyzing some of the simulations; I get 312 K, 310 K or 308 K instead of 300K (the t_ref value for the whole system). 1. What is the reason for the increase of temperature? For example it can be cutoff artifacts. What else can be? 2. To get the the error small tau_t can be reduced. What is the minimum value for tau_t? Sometimes, the pressure in the output files is high ( 7 bar, 6 bar or 1.5 bar instead of 1 bar). I.The reason for this? II. tau_p can be reduced as temperature. And what is the minimum value for tau_p? Briefly, what could be the reasons for the increase in temperature or pressure? What are your suggestions for the solution? Thanks in advance -- Ahmet Yıldırım -- 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] increase of temperature or pressure
On Wed, Dec 19, 2012 at 11:27 PM, Ahmet yıldırım ahmedo...@gmail.comwrote: Dear users, When analyzing some of the simulations; I get 312 K, 310 K or 308 K instead of 300K (the t_ref value for the whole system). 1. What is the reason for the increase of temperature? For example it can be cutoff artifacts. What else can be? Any kind of integration inaccuracy could lead to heating, e.g. too large a time step. The time period after equilibration over which you observed the average temperature, and the size of the system is a necessary part of reporting a temperature, else it's meaningless. Too little time or an average over too few atoms leads to large fluctuations and thus low expectations that the average of the sample will be correct. 2. To get the the error small tau_t can be reduced. What is the minimum value for tau_t? That's probably treating the symptoms, not the disease. Sometimes, the pressure in the output files is high ( 7 bar, 6 bar or 1.5 bar instead of 1 bar). I.The reason for this? II. tau_p can be reduced as temperature. And what is the minimum value for tau_p? See GROMACS webpage on pressure coupling and measuring pressure. Manual discussion also. Briefly, what could be the reasons for the increase in temperature or pressure? What are your suggestions for the solution? Follow protocols in publications that discussed how and why they chose their settings for the force field of interest, or which demonstrated their choices were good. Making things up, or copying others blindly is a recipe for wasting computer time. 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] High density after NPT
Hi, I am trying to simulate a short protein (160aa) in water and after 500ps NPT equilibration I got rather high value for density: average is 1014 and pretty stable around this value, but quite noisy (peaks 1010-1020). Also the pressure is very noisy with average about -7 (I am not sure it is that bad since the fluctuations there are really big). I used the AMBER03 FF with these settings for temperature and pressure coupling: ; Temperature Coupling tcoupl = V-rescale tc_grps = ProteinNon-Protein tau_t = 0.1 0.1 ref_t= 300 300 ; Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 2.0 compressibility= 4.5e-5 ref_p = 1.0 refcoord_scaling = com Previously made 100ps NVT equilibration (with modified Berendsen) gave stable and quiet 300K. What might be a problem here (if any)? Would it be better if I used Nose-Hoover thermostat for temperature coupling (I suppose no as they both are expected to give corrected ensembles)? Thank you. -- View this message in context: http://gromacs.5086.n6.nabble.com/High-density-after-NPT-tp5003950.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond index
Ok thank you. kavya On Wed, Dec 19, 2012 at 10:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/19/12 11:43 AM, Kavyashree M wrote: Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off. Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. You see a difference likely because you are invoking the command incorrectly (with overlapping index groups) and it is affecting the way the donor and acceptor arrays are constructed. The proper method of analysis is to monitor H-bonds within group 18 and then between group 18 and whatever part of the protein that does not overlap with it. -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/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] Pre-equilibrated CHARMM lipid bilayers
Peter, so as I understood after the integration of the CGenFF params into the charm36 rtp ligand ( in complex with the protein) might be parametrized just by pdb2gmx. Does this correct ? James 2012/12/20 Peter C. Lai p...@uab.edu: I am not 100% sure how the differences in c36 will affect the parameters you get from SwissParam. Personally I prefer to use ParamChem (CHARMM's version of Swissprot) to give me ligand parameters using CGenFF atomtypes, since I have CGenFF merged into my Charmm36 forcefield in gromacs. On 2012-12-19 10:37:40AM +0300, James Starlight wrote: Peter, many thanks! Could you tell me is there any differences in atom types between charmm27 and charmm36 ff? I'd like to simulate receptor-ligand complex in that bilayer where ligand molecule would be parametrized by Swiss-param ( make topology for the ligands in charmm27 ff). So because receptor and bilayer will be parametrized in charmm36 I'm not sure about proper working of Swiss's topology with that complex. James 2012/12/19 Peter C. Lai p...@uab.edu: http://cesium.hyperfine.info/~peter/gromacs/popc36/ has a fully gromacs compatible charmm36 238 POPC bilayer with 21524 waters On 2012-12-18 09:07:22PM -0800, James Starlight wrote: Justin, thanks again. As I understood gromacs already had had parameters for charmm lipid so the main approach is to do ITP file for 1 lipid by means of pdb2gmx isnt it? By the way is there any way to convert PSF or CRD file to PDB? I've found suitable bilayer for my simulation but it lack such coordinates. POPE Bilayer (310.15K, A=65.2 Â/lipid, 10ns, 340 lipids, noLRCs): CHARMM PSF, X-Plor/NAMD PSF, and CHARMM CRD James 2012/12/18, Justin Lemkul jalem...@vt.edu: On 12/18/12 2:02 PM, James Starlight wrote: Dear Gromacs Users! I'm looking for 150-200 lipid bilayer ( POPC or POPE) parametrized in charmm27 or charmm36 force field and pre-equilibrated in NPT conditions. I'll bevery thankfull to anybody who provide me with the coordinates as well as itp file for such bilayer. http://terpconnect.umd.edu/~jbklauda/research/download.html Google is your friend. There are plenty more places to look. A search for POPC CHARMM membrane coordinates (without the quotes) does the trick. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 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
