Re: [gmx-users] pbc and tpr file
Hi Tang, It doesn't hurt to check (i.e. you should check ;)) whether the .tpr file contains the protein in one piece, if you want to use it as a reference structure for rmsd calculations. You can extract the coordinates from the .tpr file using editconf and then have a look. Actually, you should've done this prior to removing jumps from the trajectory, since you must be sure to remove the jumps in the right way (check the archives for more discussion on these issues). Cheers, Tsjerk On Dec 12, 2007 1:42 AM, Mark Abraham [EMAIL PROTECTED] wrote: tangxuan wrote: hi all, I want to calculate the rmsd of my protein. If I remove the jump in the xtc file or trr file, what should I do with tpr file? Nothing. Depending on your inputs to g_rms, it might provide your reference structure. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Hi Eric, thanks a lot for clarifying this. I suspect that getting a resonable transition temperature between liquid and gel phase might be rather challenging...but yes, as you said, would be interesting... Cheers, Jochen Eric Jakobsson wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing
Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions
On Wed, 12 Dec 2007, Claus Valka wrote: Dear Sir, I would try to be more precise. example1 mdp file: rlist = (greater or equal to rvdw) vdw-type = Switch rvdw-switch=5.56 rvdw=8.9 are you aware that gromacs usues nm for distance? you can find the functional form of the shift/switch function in the manual. Between the value 5.56 and 8.9 gromacs uses cubic spline? example2 mdp file: rlist=5.56 vdw-type = Cut-off rvdw-switch=0 (this value here should be irrelevant) rvdw=8.9 Gromacs uses cubic spline after the value 8.9 till LJ to go to zero? And which is the difference of rlist if someone uses vdw-type = Cut-off instead of vdw-type = Switch? It would have been nice to have images of these options so as to be better understood. Because it is stated in the manual: rlist: (1) [nm] cut-off distance for the short-range neighbor list and also: Switch ...The neighbor search cut-off rlist should be 0.1 to 0.3 nm LARGER than rvdw... Isn't this a little bit contradictive? As far as twin cutoffs are concerned if we want to find out the total energy of the non bonded interactions we have to add LJ-14 + LJ(SR) + LJ(LR)? With tabulated potentials can I use different cutoffs for different types of atoms? Judging from your answer about system wide cutoffs I understand that even though I might use tabulated potentials, I won't be able to use different cutoffs for the different types of atoms I have. Am I correct? Yours Sincerely, Nikos --- Mark Abraham [EMAIL PROTECTED] schrieb: Claus Valka wrote: Hello, 3rd question: Which is the difference between the S(hort)R(ange) LJ and LJ 1-4? For me the short range interactions are the 1-4LJ, yet it seems that this is not the case. GROMACS uses twin-range cutoffs (see manual), so LJ-SR is inside the shorter cutoff, and LJ-LR is outside. 4th question: I want after 1,45*#963; till 2,33*#963; to use the cubic spline in such a way that the LJ potential will go smoothly to zero at 2,33#963;. If I use the biggest #963; I have, then in the mdp file rvdw-switch=5.56 and rvdw=8.9. Between these two values does the cubic spline work as a switch function using vdw-type = Switch ? Please find a way to describe your problem with plain ASCII text. 5th question: Given the above if I use vdw-type =Cut-off and rvdw=8.9 then gromacs will use cubic spline till the LJ will reach zero for a value greater than 8.9, yet to me uknown? If this is not the case how LJ goes to zero with this option? I don't understand what you're asking. 6th question: If I want to use a quintic spline between 1,45*#963; till 2,33*#963;(cut-off value) for the different combination of atoms(they have different #949; and #963;), then should I use a tabulated potential? And if I do that which will be the meaning of cutoffs in the mdp file as I would like them to be different for each of the different types of atoms I have? Can I use different cut-offs for the different types of atoms I have? The cut-offs are a system-wide property. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Jetzt Mails schnell in einem Vorschaufenster überfliegen. Dies und viel mehr bietet das neue Yahoo! Mail - www.yahoo.de/mail ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] asking for recommendations
Hi! I am a student currently using GROMACS (which I am new at) for a study on iota-carrageenan. The starting structures used are already in a double helix configuration. One file contains two ten-monomer iota-carrageenan chains coiled into a double helix; the other two files (differing only in the arrangement of the helices) consist of three double helices, each helix consists of two six-monomer chains. These were simulated at two conditions - high temp and room temp - for 20 ns each. The double helix should theoretically uncoil. However, no such uncoiling was observed. I was tasked to perform analysis tools to possibly provide other reasons for the observed results apart from modeling limitations (i.e. relatively short length and simulation time). As of the moment, I am doing g_hbond for h-bond analysis. Could you please recommend other analysis tools that are likely to be useful in my research? Thank you! _ Get your free suite of Windows Live services today! http://www.get.live.com/wl/all___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Yes, this should be attempted. Perhaps the ultimate test of a force field is to nail a phase change. At 03:34 AM 12/12/2007, you wrote: Hi Eric, thanks a lot for clarifying this. I suspect that getting a resonable transition temperature between liquid and gel phase might be rather challenging...but yes, as you said, would be interesting... Cheers, Jochen Eric Jakobsson wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany
Re: [gmx-users] asking for recommendations
Hi Michelle, What reasons do you have suggesting factors other than modelling limitations? Is there experimental data regarding the time scale of uncoiling? I would guess it would take longer than 20 ns. Also, you should consider that you're looking at a single molecule. The observation of uncoiling in vitro or in silico involves many molecules, of which one may stay coiled for a long time (maybe the one you're looking at in your simulation). You might try to express the properties of your helix in terms of number of hydrogen bonds, helix length, helix radius and helix bending, in which you could observe trends towards more loose states, suggesting the onset of uncoiling. But it would also be better to try and extend the simulations. Cheers, Tsjerk On Dec 12, 2007 9:57 AM, michelle yap [EMAIL PROTECTED] wrote: Hi! I am a student currently using GROMACS (which I am new at) for a study on iota-carrageenan. The starting structures used are already in a double helix configuration. One file contains two ten-monomer iota-carrageenan chains coiled into a double helix; the other two files (differing only in the arrangement of the helices) consist of three double helices, each helix consists of two six-monomer chains. These were simulated at two conditions - high temp and room temp - for 20 ns each. The double helix should theoretically uncoil. However, no such uncoiling was observed. I was tasked to perform analysis tools to possibly provide other reasons for the observed results apart from modeling limitations (i.e. relatively short length and simulation time). As of the moment, I am doing g_hbond for h-bond analysis. Could you please recommend other analysis tools that are likely to be useful in my research? Thank you! _ Get your free suite of Windows Live services today! http://www.get.live.com/wl/all___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] rvdw vs cut-off / different types of non bonded interactions
Dear Sir, I'm absolutely aware that gromacs uses nm for distance. The values should be 0.556 and 0.89. I used them only for reference purposes and I hope that this didn't cause any misanderstanding so as to point me to the manual. If this is the case of not understanding my questions, I deeply appologize. Yours Sincerely, Nikos --- David van der Spoel [EMAIL PROTECTED] schrieb: On Wed, 12 Dec 2007, Claus Valka wrote: Dear Sir, I would try to be more precise. example1 mdp file: rlist = (greater or equal to rvdw) vdw-type = Switch rvdw-switch=5.56 rvdw=8.9 are you aware that gromacs usues nm for distance? you can find the functional form of the shift/switch function in the manual. Between the value 5.56 and 8.9 gromacs uses cubic spline? example2 mdp file: rlist=5.56 vdw-type = Cut-off rvdw-switch=0 (this value here should be irrelevant) rvdw=8.9 Gromacs uses cubic spline after the value 8.9 till LJ to go to zero? And which is the difference of rlist if someone uses vdw-type = Cut-off instead of vdw-type = Switch? It would have been nice to have images of these options so as to be better understood. Because it is stated in the manual: rlist: (1) [nm] cut-off distance for the short-range neighbor list and also: Switch ...The neighbor search cut-off rlist should be 0.1 to 0.3 nm LARGER than rvdw... Isn't this a little bit contradictive? As far as twin cutoffs are concerned if we want to find out the total energy of the non bonded interactions we have to add LJ-14 + LJ(SR) + LJ(LR)? With tabulated potentials can I use different cutoffs for different types of atoms? Judging from your answer about system wide cutoffs I understand that even though I might use tabulated potentials, I won't be able to use different cutoffs for the different types of atoms I have. Am I correct? Yours Sincerely, Nikos --- Mark Abraham [EMAIL PROTECTED] schrieb: Claus Valka wrote: Hello, 3rd question: Which is the difference between the S(hort)R(ange) LJ and LJ 1-4? For me the short range interactions are the 1-4LJ, yet it seems that this is not the case. GROMACS uses twin-range cutoffs (see manual), so LJ-SR is inside the shorter cutoff, and LJ-LR is outside. 4th question: I want after 1,45*#963; till 2,33*#963; to use the cubic spline in such a way that the LJ potential will go smoothly to zero at 2,33#963;. If I use the biggest #963; I have, then in the mdp file rvdw-switch=5.56 and rvdw=8.9. Between these two values does the cubic spline work as a switch function using vdw-type = Switch ? Please find a way to describe your problem with plain ASCII text. 5th question: Given the above if I use vdw-type =Cut-off and rvdw=8.9 then gromacs will use cubic spline till the LJ will reach zero for a value greater than 8.9, yet to me uknown? If this is not the case how LJ goes to zero with this option? I don't understand what you're asking. 6th question: If I want to use a quintic spline between 1,45*#963; till 2,33*#963;(cut-off value) for the different combination of atoms(they have different #949; and #963;), then should I use a tabulated potential? And if I do that which will be the meaning of cutoffs in the mdp file as I would like them to be different for each of the different types of atoms I have? Can I use different cut-offs for the different types of atoms I have? The cut-offs are a system-wide property. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Jetzt Mails schnell in einem Vorschaufenster überfliegen. Dies und viel mehr bietet das neue Yahoo! Mail - www.yahoo.de/mail ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gel Phase in DMPC using Berger force field ??
Dear all, For the gel-to-liquid crystalline phase transition in DPPC and DPPE there is a paper: Leekumjorn and Sum, BBA, 1768 (2007) 354-365 I've found it several month ago and I haven't red through it completely, but they used the Berger force field. Best, Zoltan Eric Jakobsson [EMAIL PROTECTED] wrote: Yes, this should be attempted. Perhaps the ultimate test of a force field is to nail a phase change. At 03:34 AM 12/12/2007, you wrote: Hi Eric, thanks a lot for clarifying this. I suspect that getting a resonable transition temperature between liquid and gel phase might be rather challenging...but yes, as you said, would be interesting... Cheers, Jochen Eric Jakobsson wrote: Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric At 10:22 AM 12/11/2007, you wrote: Hi Steffen, thanks a lot for your reply. -what are your VdW cutoffs? Berger lipids absolutely need the 0.8/1.4 nm twin range cutoff for working properly. Are you using PME for electrostatics? I used a LJ-cutoff at 1.0nm. That's what was used for the original Berger-Paper (*O Berger, O Edholm and F Jähnig, */Biophysical Journal/ 72: 2002-2013 (1997). Shouldn't this be all right? And I used PME (which was indeed not used in the original work. -how did you set up the pressure coupling? I used weak coupling (tau=1.0ps) -900 waters are not really much, the head groups will probably interact with their mirror images due to pbc. Try a lot more (thought about 1?) for having a real bilayer in a solution. I also tried with more water, the gel phase did not appear either. From my experience, the Berger lipids are well defined for a specific temperature, but if you go up/down the temperature scale, they are not really following the experimental values/phase behaviour. By the way: experimental data on lipid order parameters varies considerably throughout the complete literature, so don't rely onto that too much as well. Sorry for giving more questions than answers, but that's the shitty part with lipid bilayers in MD... Steffen Thanks again, Jochen -- Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - Eric Jakobsson, Ph.D. Professor, Department of Molecular and Integrative Physiology, and of Biochemistry, and of the Center for Biophysics and Computational Biology Senior Research Scientist, National Center for Supercomputing Applications Professor, Beckman Institute for Advanced Science and Technology 3261 Beckman Institute, mc251 University of Illinois, Urbana, IL 61801 ph. 217-244-2896 Fax 217 244 9757 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
[gmx-users] problem using makehole program
Dear All i started makehole program...but am facing problems setting the mdp parameters. when i gave mdrun command i get an error..that i cant make out: the command i gave is:- /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun -v -hole -holep hpgr.mdp -s dmpc_water_1ns.tpr -o cecmel311334_dmpc_hole_1ns.trr -c cecmel311334_dmpc_hole_1ns.gro -e cecmel311334_dmpc_hole_1ns.edr -g cecmel311334_dmpc_hole_1ns.log WARNING 1 [file , line 1]: Unknown left-hand molsurf_log in parameter file Reading ASCII grasp surface atomic surface: allocating list of nn vertex of each of 16853 atoms atomic surface: reading surface data from file grasp_sur_ascii atomic surface: reading 6712 vertices and normals and 13420 triangles...done Back Off! I just backed up gsurf.log to ./#gsurf.log.1# starting mdrun 'dmpc $ 3655 water in constant area 0.596' 50 steps, 1000.0 ps. Back Off! I just backed up cecmel311334_dmpc_hole_1ns.trr to ./#cecmel311334_dmpc_hole_1ns.trr.2# Back Off! I just backed up insidesurf.pdb to ./#insidesurf.pdb.2# Fatal error: Don't worry, this is in fact a normal stop in debugsurf mode: now check insidegr.pdb and molsurfpdb.pdb And when i try to open molsurfpdb.pdb...vmd shows error, that no of bonds is too much. so the file doesnt open. and 'insidegr.pdb' named file is not formed in my directory. please guide me through I am attaching the *.mdp file with this mail. regards nur - Save all your chat conversations. Find them online. hpgr.mdp Description: 3875843079-hpgr.mdp ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Methanol SOL :Number of solventmolecules = 0
Dear Dr. Xavier Periole,
Thank you for guiding me through. I could solve the problem of setting up the
system for minimization. However When started minimization run for 2000 steps
with steepest descent , I encountered yet another problem. which is as follows
..
Methanol optimization:
Started Steepest Descents on node 0 Tue Dec 11 17:48:57 2007
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps= 2000
Grid: 4 x 5 x 4 cells
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
Step Time Lambda
00.00.0
calc_bor: cg0=0, cg1=553, ncg=553
CG0[0]=0, CG1[0]=553
CG0[1]=0, CG1[1]=0
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 80 ]
Please report this to the mailing list (gmx-users@gromacs.org)
Now where do I go from here? Its asking me to energy minimize the system which
is what I am trying to do ! What is this ci value and why is it so high? Kindly
help me I am once again stuck. Furthermore, when I minimized the same peptide
in SPC216 water box of 1108 water molecules for 2000 steps this error did not
appear. When I compared the md.log files in both the cases I found that in case
of water optimization of SPC water was enabled where as this line for methanol
was missing which should mean that the energies are shooting off scale is
that right ? Should I optimize my system in vacuo before simmulating in
methanol?
Water optimization:
{Generated table with 500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 1108 molecules.
Initiating Steepest Descents
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 3396
Started Steepest Descents on node 0 Wed Dec 12 15:52:11 2007
Removing pbc first time
Done rmpbc
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps= 2000
Going to use C-settle (1108 waters)
wo = 0.33, wh =0.33, wohh = 3, rc = 0.08165, ra = 0.0384897
rb = 0.0192449, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
Grid: 4 x 5 x 4 cells}
regards
sharada
-- Original Message --
From: Xavier Periole [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Tue, 11 Dec 2007 12:07:27 +0100
Subject: Re: Fw: Re: [gmx-users] Methanol SOL :Number of solvent molecules
= 0
in your agg2t.top you should replace the last line :
SOLXXX
by:
Methanol XXX
which is the name of the molecule.
You should also remove the angle definition in methanol.itp. Placing
a ; at the beginning of the line is enough.
XAvier
On Tue, 11 Dec 2007 15:40:04 +0530 (IST)
sharada [EMAIL PROTECTED] wrote:
Dear Mark Abraham,
I have changed MeoH to SOL in .gro and .itp files and also changed the
#include line to methanol.itp
It now seemed to have written the solvent molecules in the top file with SOL
as the name with atom types of methanol.
When I ran grompp program as following I get the error as shown below: I am
also attaching the .gro,.itp,.top files. for information. Did I miss out
anything ?
grompp -f em.mdp -c agg2_b4em.gro -p agg2.top -o agg2_em.tpr
[EMAIL PROTECTED] Aggregates]$ grompp -f em.mdp -c agg2_b4em.gro -p agg2.top
-o
agg2_em.tpr
Option Type Value Description
--
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-niceint 0 Set the nicelevel
-[no]v boolyes Be loud and noisy
-time real -1 Take frame at or first after this time.
-npint 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
creating statusfile
Re: [gmx-users] pbc and tpr file
Hi, Thanks for your reply. The protein I simulated has 16 subunits. I checked the protein struture (no jump) in the tpr file and there are no contacts between each subunits. The protein structure in the fist frame of simulation seems ok, but has jumps. Two strucutres are very different and I do not why? Therefore, something strange (rotation) will happen to the system after I remove jumps in the trajectory. Do you think it is right to produce a new reference structure from the first frame by tpbconv? Thanks Tang On Wed, 2007-12-12 at 09:03 +0100, Tsjerk Wassenaar wrote: Hi Tang, It doesn't hurt to check (i.e. you should check ;)) whether the .tpr file contains the protein in one piece, if you want to use it as a reference structure for rmsd calculations. You can extract the coordinates from the .tpr file using editconf and then have a look. Actually, you should've done this prior to removing jumps from the trajectory, since you must be sure to remove the jumps in the right way (check the archives for more discussion on these issues). Cheers, Tsjerk On Dec 12, 2007 1:42 AM, Mark Abraham [EMAIL PROTECTED] wrote: tangxuan wrote: hi all, I want to calculate the rmsd of my protein. If I remove the jump in the xtc file or trr file, what should I do with tpr file? Nothing. Depending on your inputs to g_rms, it might provide your reference structure. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] literature on GROMOS96 43b1 force field and vacuum simulations
On Wed, 12 Dec 2007 11:24:01 +0100 Carsten Baldauf [EMAIL PROTECTED] wrote: dear all// i am looking for literature describing the gromos 96 force fields, especially the vacuum force field 43b1. unfortunately i don't find much besides the gromos manual ... look for gromos force field you should find it easily. You can also go to the web page of van Gunsteren's group at the ETH. do you have any suggestions/hints? thank you very much// carsten p.s.: just in case you would want to perform a md simulation of a peptide/protein in vacuum, which force field would you choose and why? Depends what you want to do with the simulation. However in a general manner there are no force field that is known to describe a protein/peptide in vacuum with any relative realism. -- dr carsten baldauf biotechnologisches zentrum der tu dresden http://www.biotec.tu-dresden.de/pisabarro http://www.biotec.tu-dresden.de/~carstenb Molecular Docking, Complexity, and Optimization See http://pacosy.informatik.uni-leipzig.de/MDCO-2007/ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html No Software Patents! See http://www.ffii.org/index.en.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Is there any way to do r^3 distance dependence?
Hi, all, I know that Gromacs has the capability of restraining a molecule with r^6 distance dependence. Is there any way to do r^3 distance dependence? Best wishes, Art Roberts University of Washington Department of Medicinal Chemistry Seattle, WA 98195 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Diagnosing an explosion
Apologies for replying to myself - maybe I can sharpen up some of my original questions below: Reply below I am having a problem with my BD simulation either crashing with a Range error or locking up the mdrun process completely. I am running Gromacs 3.3.1 (must use this version ATM because HPC provider has not upgraded yet) on a quad core Intel machine, w/ Fedora Core 7. I have 1000 'particles' in a cubic box (configuration here: http://datavet.hv.se/personal/SK/publicfiles/colloid.pdb where the particles are placed randomly with no two particle centres closer than 4 nm. The particles are defined in the topology here: ; Complete topology file ; ; particles.itp [ defaults ] 1 1 no 1.0 1.0 [ atomtypes ] AR 28699.81134 0.00 A 1.0 1.0 Looks like you are using dimensionless eps and sigma while using otherwise MD units (e.g. T). Check chapter 2 of the manual. You want to multiply your T by boltz (0.008314 or something like that) probably. Aha! Thank you David. My goal was to use MD units in everything, since my tabulated data file was extracted from another GROMACS simulation and is hence already in MD units (kJ/mol vs. nm), and I would prefer to specify temperatures in K. My reason for specifying 1.0 for the last two parameters was that I thought this would allow me to use, unscaled, the tabulated potential (which is already in MD units). If I want to do this, what alternative values should I use for the last two parameters on the [ atomtypes ] line above (given that I am really only using the g(r) and g''(r) columns to hold my potential data: the h(r) and h''(r), which I don't care about, are all zeroes) ? If I change the combination type to 2 or 3 in the [ defaults ] line, will this remove the unit scaling problem ? I have checked Chapter 2 in the manual and I am still unsure how to handle this. I took your advice (which matches with manual Section 2.4 on *reduced* units) and scaled my temperature to 2.494353 = 300K * 0.008314. This did not give a crash, but increasing the timestep and decreasing bd_fric made the problem return. Scaling the temperature value in this way did not fix the 'equilibration around 2x requested temperature' problem mentioned below - g_energy still shows the temperature settling at a numerical value around 4.988. Can anyone suggest a reason for this strange thermostat behaviour ? Many thanks, Steve Kirk -- Dr. Steven R. Kirk [EMAIL PROTECTED], [EMAIL PROTECTED] Dept. of Technology, Mathematics Computer Science (P)+46 520 223215 University West (F)+46 520 223299 P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gel Phase in DMPC using Berger force field ?? -- Focus: naming convention
Several points: What is called the Berger force field was actually developed by See-Wing Chiu in our lab and presented in a 1995 paper. The Berger et al paper tested this force field against another candidate and found that it was better, and that is the paper that has been cited ever since. I agree that it is incorrect to refer to this as the Berger forcefield, although I have myself referred to it in this way for informal discussions. If one were to discuss the important contributions I would refer to the following papers (Jorgensen_1988/Egberts_1994/Chiu_1995/Chiu_1996/Berger_1997), and of course the Ryckaert-Bellemans contribution is also important. Perhaps I have missed some, but in that case it is not intentional. I would be interested to participate in a discussion about the naming convention for these parameters. For example, it is unclear to me why one would refer to them as the 'Chiu parameters' as opposed to the 'Egbert parameters', or even the 'Ryckaert-Bellemans lipid parameters'. I would also accept an acronym from the first authors such as RBJECB. For detailed methods sections I am in the habit of referring to it by a chronological sentence as opposed to by a short name, but for informal discussion a short name is certainly convenient. To be clear, I am not arguing against calling then the 'Chiu parameters' but would be in favour of more discussions on the topic. Chris. See-Wing did tests of the necessary VDW cut-off for accuracy against what seemed like the most sensitive test, the value of the dipole potential at the water-lipid interface, and concluded that one should use a cut-off of at least 18 angstroms. The van der Waals parameters for the hydrocarbon tails were reparameterized in a paper we published a few years ago, and in that paper we verified that the 18 angstrom cutoff was required for an accurate liquid hydrocarbon simulation also. Recently See-Wing has reparameterized the van der Waals parameters in the lipid head groups, using specific volumes of liquids comprised of small molecules that are part of the head group. The resulting force fields, which retain the partial charges of the Berger-Chiu field, work very well in replicating x-ray structure factors of lipids with various chain compositions, but he has not yet tried to do gel phase--that would be interesting. The journal ms. is still sitting on my desk, I am afraid, but there is a pretty good description of the parameterization in a chapter in a book that Scott Feller is editing, which we can send on request, as well as the lipid complete force field in itself. We believe it is state of the art at this time. Best, Eric ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] is there performance data for GROMACS on Blue Gene/L?
Does anybody have access to any performance data for GROMACS on a Blue Gene/L system? I'm putting together a proposal for some time on such a machine, and some moderately accurate costings would be nice. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Density Deferences between spc216 and tip4p water models
Dear All, I was trying create a box (cubic 10 10 10) of water. I am a bit surprised by looking at the density deferences between spc216 and tip4p water models. I am giving the brief output below. genbox -cs tip4p.gro -box 10 10 10 Output configuration contains 131540 atoms in 32885 residues Volume :1000 (nm^3) Density: 1639.65 (g/l) Number of SOL molecules: 32885 genbox -cs spc2i6.gro -box 10 10 10 Output configuration contains 99678 atoms in 33226 residues Volume :1000 (nm^3) Density: 993.966 (g/l) Number of SOL molecules: 33226 What would be the reason for this drastic differences in density? How can I make it into 1000 (g/l) by using above command. Thanks in advance. Regards Chandu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
