Re: [gmx-users] How to use deuterium order parameters
On Wed, Nov 2, 2011 at 2:06 PM, Alex alexbioi...@yahoo.com wrote: Dear All I'd like to perfom a deuterium oerder parameters analysys in a system with DPPC + Protein + Water I read that I've to make an index file that contains one group each for every carbon atom in the acyl-chain (starting with the carbonyl-carbon and going further down). Where can I get carbon atoms index in the acyl-chain to group them? Have I to open the DPPC in pdbviewer yes, that's a way to do it. I need as well to make two index files: for sn1 and sn2 chains of DPPC. yes, that is correct. Have I to run g_order in both ndx files (sn1 and sn2)? yes, that is also correct. make sure to write two different output files (sn1.out and sn2.out) 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 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] water box size from output files
rabab, justin mentioned the *gro file saved at the end of the simulation - the last line contains the box dimensions. you can extract them with g_energy: g_energy -f your_edr_file -o your_output_file and then selecting: Box-X Box-Y Box-Z good luck, igor Igor Marques On Mon, Jul 25, 2011 at 5:07 PM, Rabab Toubar rtou...@yahoo.com wrote: Thanks Justin for your reply. But what is the extension of the output coordinate file. And for the .edr file it failed to open in windows; how can I possibly view it Thanks Rabab Toubar --- On Mon, 7/25/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] water box size from output files To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, July 25, 2011, 11:15 AM Rabab Toubar wrote: Hi I was wondering if there is a way to determine the water box size from the output files after the simulation run is over Box vectors are printed to the output coordinate file (final snapshot) and can be extracted from along the trajectory from the .edr file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC
thomas, i've recently placed a similar question and justin asked me to show my index for the double bound calculation, so, i'm asking you the same. you should have Ci-1 Ci - the first carbon of the double bound Ci+1 - the second carbon of the double bound Ci+2 in that index doing this, for C9 and C10 i've obtained the following values 0.0738068 -0.000533683 that you should then replace in the correct positions in the sn2 output good luck, and sorry if i'm missing the point :| igor Igor Marques On Wed, Jun 8, 2011 at 5:53 PM, Thomas Piggot t.pig...@soton.ac.uk wrote: Hi Everyone, I am facing a problem when calculating the lipid deuterium order parameters for the unsaturated carbons of the sn-2 tail of POPC using g_order with GROMACS version 4.5.4 (although I have tried other older versions too but they all give the same results). Firstly, I should say the the calculation of the order parameters for the saturated sn-1 chain (and also both chains of DPPC) behave as I would expect, and produce order parameters that compare well to previously published simulations and experimental values. To calculate the order parameters of the unsaturated chain I am following the approach as given on the GROMACS website ( http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order), so splitting the calculation into two parts for the saturated and unsaturated regions of the chain. The problem I am facing is that the order parameter for carbon 9 (so the first carbon in the double bond), calculated using the -unsat option, is much larger than expected. By this I mean that for the two different force fields I have tested (namely the CHARMM36 parameters of Klauda et al., and the GROMOS 53A6L parameters of Poger et al.) the order parameter for this carbon is much larger than the published simulation values and also much larger than experimental values. To highlight this, I have just put the numbers I have obtained using g_order for this carbon below, and compared to some rough values I have estimated from figures provided in the Klauda and Poger papers: CHARMM36 g_order:0.133732 Klauda estimate:0.06 GROMOS53A6L: g_order:0.199651 Poger estimate: 0.07 Myself and a colleague have tried looking into the code to determine how the order parameters are calculated using the -unsat option, however we couldn't quite follow the calculation. Hopefully someone who knows something more about g_order can help with this problem. Again I should stress that it appears that the main difference in order parameters between what I have calculated and the published ones is just in this one carbon, for both force fields. A similar issue to this has also been reported previously on the list for this carbon of POPC using the 'Berger' force field ( http://lists.gromacs.org/pipermail/gmx-users/2010-February/049072.html). Thank you for any help anyone can give Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] electron density
dear all, regarding the matter of electron density, can anyone clarify me on the output units? from this discussion i understand the values are presented in electrons/A^3 - is this correct? best regards, igor Igor Marques Molecular Modeling Group – Univ. of Aveiro http://molecular-modeling.dq.ua.pt/ On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian jianhuit...@gmail.com wrote: Problem solved. The 2 in the text is just a typo when I sent the email. So actually there is no partial charge in the electrons.dat file. Thanks, Justin. Jianhui Date: Sat, 01 Jan 2011 13:56:45 -0500 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4d1f78ed.5070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Date: Fri, 31 Dec 2010 19:08:50 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I How much smaller? I got about 0.27 e/A^3. am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Possibly, but without seeing what you used for input, information about your simulation, etc it's impossible to say. In the electrons.dat file, I had 2 OW = 8.834 HW1 = 0.583 HW2 = 0.583 And then used g_density ... -ei electrons.dat -dens electron ... There are several problems. The first line of electrons.dat indicates there are only two unique atom names, but clearly you're supplying three. Second, this file is read in such that at integral number of electrons is detected on each line. So, in your case, two lines are being read, one that detects 8 electrons, and another that detects zero. -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
Re: [gmx-users] electron density
thanks mate! Igor Marques On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: Igor Marques wrote: dear all, regarding the matter of electron density, can anyone clarify me on the output units? from this discussion i understand the values are presented in electrons/A^3 - is this correct? No. It is electrons/nm^3. Standard units are defined in Chapter 2 of the manual (and printed in the code, of course). -Justin best regards, igor Igor Marques Molecular Modeling Group – Univ. of Aveiro http://molecular-modeling.dq.ua.pt/ On Sat, Jan 1, 2011 at 9:01 PM, Jianhui Tian jianhuit...@gmail.commailto: jianhuit...@gmail.com wrote: Problem solved. The 2 in the text is just a typo when I sent the email. So actually there is no partial charge in the electrons.dat file. Thanks, Justin. Jianhui Date: Sat, 01 Jan 2011 13:56:45 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d1f78ed.5070...@vt.edu mailto:4d1f78ed.5070...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Date: Fri, 31 Dec 2010 19:08:50 -0500 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] electron density To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu mailto:4d1e7092.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Jianhui Tian wrote: Hi gmx users, I tried to calculate both the mass density and electron density for the water layer of a membrane simulation. The mass density is 1000 kg/m^3, however the electron density I got is smaller than about 0.33 e/A^3. I How much smaller? I got about 0.27 e/A^3. am using a CHARMM force field and the CHARMM version of TIP3P water. Am I doing anything wrong when calculating the electron density? Thanks a lot. Possibly, but without seeing what you used for input, information about your simulation, etc it's impossible to say. In the electrons.dat file, I had 2 OW = 8.834 HW1 = 0.583 HW2 = 0.583 And then used g_density ... -ei electrons.dat -dens electron ... There are several problems. The first line of electrons.dat indicates there are only two unique atom names, but clearly you're supplying three. Second, this file is read in such that at integral number of electrons is detected on each line. So, in your case, two lines are being read, one that detects 8 electrons, and another that detects zero. -Justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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_order output is mirrored
dear all, after justin contribution, the SN2 chain plot now looks a little different: [image: sn2_new.png] http://imm.io/5JAZ the real matter of this e-mail, although i really appreciate the help justin has provided regarding the proper use of this tool, is the fact that my plot looks mirrored from the one i've previously referred, from Jojart and Martinek -- http://i.imm.io/5IGl.png forgetting, for now, the SN2 chain, harder to analyse, what i really found weird is the fact that SN1 is mirroring the published results: [image: sn1_new.png] http://imm.io/5JCi so, for segment 2, the first they analyze, in the filled triangle line the value is around 0.35, while for the 14th segment the value is about 0.28. in my case, the order is the other way around! my SN1 starts with a low value that is increased through the chain! (0.24 -- 0.29). should i change the order of the chain in the index files? although that makes the plot resemble the ones already published, i don't think that is the definitive solution to this problem! (this applies also to the DMPC chains of my colleague) best regards! igor Igor Marques On Tue, May 17, 2011 at 9:47 PM, Igor Marques igor.drago...@gmail.comwrote: Igor Marques On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: Igor Marques wrote: snip 2. Can you post your .ndx file? for sn1 chain: Reading structure file Going to read 1 old index file(s) Not exactly what I was going for (I wanted to see the contents of the .ndx file), but... 0 C12__r_1-72:72 atoms 1 C29__r_1-72:72 atoms 2 C30__r_1-72:72 atoms 3 C31__r_1-72:72 atoms 4 C32__r_1-72:72 atoms 5 C33__r_1-72:72 atoms 6 C34__r_1-72:72 atoms 7 C35__r_1-72:72 atoms 8 C36__r_1-72:72 atoms 9 C37__r_1-72:72 atoms 10 C38__r_1-72:72 atoms 11 C39__r_1-72:72 atoms 12 C40__r_1-72:72 atoms 13 C41__r_1-72:72 atoms 14 C42__r_1-72:72 atoms Here you only have 15 carbons. The sn-1 (palmitoyl) should be 16. for sn2 chain: Reading structure file Going to read 1 old index file(s) 0 C9__r_1-72 :72 atoms 1 C13__r_1-72:72 atoms 2 C14__r_1-72:72 atoms 3 C15__r_1-72:72 atoms 4 C16__r_1-72:72 atoms 5 C17__r_1-72:72 atoms 6 C18__r_1-72:72 atoms 7 C19__r_1-72:72 atoms 8 C20__r_1-72:72 atoms 9 C21__r_1-72:72 atoms 10 C22__r_1-72:72 atoms 11 C23__r_1-72:72 atoms 12 C24__r_1-72:72 atoms 13 C25__r_1-72:72 atoms 14 C26__r_1-72:72 atoms 15 C27__r_1-72:72 atoms 16 C28__r_1-72:72 atoms And the same here - 17 groups instead of 18. I'm not familiar with the numbering, but it seems odd to jump from, e.g., C9 to C13 - are you sure your first carbon (C9) is not in the glycerol backbone rather than the ester? i'll also take a careful look into this! and the numbering is just like this. don't ask! ;) 3. What is your command for the sn-2 chain? You cannot obtain unsaturated and saturated order parameters in the same command. You must do them separately, and the index groups are different. For instance, to get the order parameters around the unsaturation, your index file should contain only Cn-1, Cn, Cn+1, Cn+2, where Cn and Cn+1 are the C atoms joined by the double bond. Then run g_order with the -unsat option. These values can then replace the corresponding carbon positions in the g_order output of the whole sn-2 chain. If done improperly, you can get weird results. the command is actually the same with the apropriate index file... maybe this is the problem for POPC - i'll look at it carefully! Then this is certainly a problem. i'll look at it with my colleague. if our problem persists, we'll get back in touch! thanks again! ^^ 4. What are the simulation conditions? Are you trying to replicate the published work? Different simulations conditions will certainly impact the structural parameters, and insufficient sampling can give weird looking curves, as well. All it might mean is that your data are not yet well-converged. NPT, surface tension of 40 dyn/cm, t=310 K, GAFF force field. the plot represents the last 10 of 150 ns of production - however, it presents the same behavior in longer (200 ns) simulations! I'd suspect the index file(s) and/or g_order commands rather than convergence issues, in this case. -Justin thanks! -Justin best regards and thanks in advance! Igor Marques -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar
[gmx-users] g_order output is mirrored
dear all, i've been trying to use g_order to analyse the disorder of the chains of POPC model membrane simulations, namely the SCD parameters. one example of desired output is this: [image: 5IGl.png] http://i.imm.io/5IGl.png - Performance of the general amber force field in modeling aqueous POPC membrane bilayers by Balázs Jójárt Tamás A. Martinek DOI: 10.1002/jcc.20748 however, my output, when plotted, presents a looks like mirrored: [image: deuter.png] http://i.imm.io/5IGK.png my input index files start with the first carbon after the c=o in each chain, as in the tutorial - http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html if started the other way around, the plot resembles published data... a colleague tried the same process with a DMPC membrane model and his plots are also mirrored. our command line: g_order -f ../TRAJECTORY.xtc -s ../TOPOLOGY.tpr -n INDEX_CHAIN_sn1.ndx -od OUTPUT_SCD.xvg what are we not doing/doing wrong? best regards and thanks in advance! Igor Marques deuter.png-- 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_order output is mirrored
Igor Marques On Tue, May 17, 2011 at 8:04 PM, Justin A. Lemkul jalem...@vt.edu wrote: Igor Marques wrote: dear all, i've been trying to use g_order to analyse the disorder of the chains of POPC model membrane simulations, namely the SCD parameters. one example of desired output is this: 5IGl.png http://i.imm.io/5IGl.png - Performance of the general amber force field in modeling aqueous POPC membrane bilayers by Balázs Jójárt Tamás A. Martinek DOI: 10.1002/jcc.20748 however, my output, when plotted, presents a looks like mirrored: deuter.png http://i.imm.io/5IGK.png my input index files start with the first carbon after the c=o in each chain, as in the tutorial - http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html if started the other way around, the plot resembles published data... a colleague tried the same process with a DMPC membrane model and his plots are also mirrored. our command line: g_order -f ../TRAJECTORY.xtc -s ../TOPOLOGY.tpr -n INDEX_CHAIN_sn1.ndx -od OUTPUT_SCD.xvg what are we not doing/doing wrong? A few questions: 1. What version of Gromacs is this? version 4.5.3 2. Can you post your .ndx file? for sn1 chain: Reading structure file Going to read 1 old index file(s) 0 C12__r_1-72:72 atoms 1 C29__r_1-72:72 atoms 2 C30__r_1-72:72 atoms 3 C31__r_1-72:72 atoms 4 C32__r_1-72:72 atoms 5 C33__r_1-72:72 atoms 6 C34__r_1-72:72 atoms 7 C35__r_1-72:72 atoms 8 C36__r_1-72:72 atoms 9 C37__r_1-72:72 atoms 10 C38__r_1-72:72 atoms 11 C39__r_1-72:72 atoms 12 C40__r_1-72:72 atoms 13 C41__r_1-72:72 atoms 14 C42__r_1-72:72 atoms for sn2 chain: Reading structure file Going to read 1 old index file(s) 0 C9__r_1-72 :72 atoms 1 C13__r_1-72:72 atoms 2 C14__r_1-72:72 atoms 3 C15__r_1-72:72 atoms 4 C16__r_1-72:72 atoms 5 C17__r_1-72:72 atoms 6 C18__r_1-72:72 atoms 7 C19__r_1-72:72 atoms 8 C20__r_1-72:72 atoms 9 C21__r_1-72:72 atoms 10 C22__r_1-72:72 atoms 11 C23__r_1-72:72 atoms 12 C24__r_1-72:72 atoms 13 C25__r_1-72:72 atoms 14 C26__r_1-72:72 atoms 15 C27__r_1-72:72 atoms 16 C28__r_1-72:72 atoms 3. What is your command for the sn-2 chain? You cannot obtain unsaturated and saturated order parameters in the same command. You must do them separately, and the index groups are different. For instance, to get the order parameters around the unsaturation, your index file should contain only Cn-1, Cn, Cn+1, Cn+2, where Cn and Cn+1 are the C atoms joined by the double bond. Then run g_order with the -unsat option. These values can then replace the corresponding carbon positions in the g_order output of the whole sn-2 chain. If done improperly, you can get weird results. the command is actually the same with the apropriate index file... maybe this is the problem for POPC - i'll look at it carefully! 4. What are the simulation conditions? Are you trying to replicate the published work? Different simulations conditions will certainly impact the structural parameters, and insufficient sampling can give weird looking curves, as well. All it might mean is that your data are not yet well-converged. NPT, surface tension of 40 dyn/cm, t=310 K, GAFF force field. the plot represents the last 10 of 150 ns of production - however, it presents the same behavior in longer (200 ns) simulations! thanks! -Justin best regards and thanks in advance! Igor Marques -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users 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_order output is mirrored
Igor Marques On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul jalem...@vt.edu wrote: Igor Marques wrote: snip 2. Can you post your .ndx file? for sn1 chain: Reading structure file Going to read 1 old index file(s) Not exactly what I was going for (I wanted to see the contents of the .ndx file), but... 0 C12__r_1-72:72 atoms 1 C29__r_1-72:72 atoms 2 C30__r_1-72:72 atoms 3 C31__r_1-72:72 atoms 4 C32__r_1-72:72 atoms 5 C33__r_1-72:72 atoms 6 C34__r_1-72:72 atoms 7 C35__r_1-72:72 atoms 8 C36__r_1-72:72 atoms 9 C37__r_1-72:72 atoms 10 C38__r_1-72:72 atoms 11 C39__r_1-72:72 atoms 12 C40__r_1-72:72 atoms 13 C41__r_1-72:72 atoms 14 C42__r_1-72:72 atoms Here you only have 15 carbons. The sn-1 (palmitoyl) should be 16. for sn2 chain: Reading structure file Going to read 1 old index file(s) 0 C9__r_1-72 :72 atoms 1 C13__r_1-72:72 atoms 2 C14__r_1-72:72 atoms 3 C15__r_1-72:72 atoms 4 C16__r_1-72:72 atoms 5 C17__r_1-72:72 atoms 6 C18__r_1-72:72 atoms 7 C19__r_1-72:72 atoms 8 C20__r_1-72:72 atoms 9 C21__r_1-72:72 atoms 10 C22__r_1-72:72 atoms 11 C23__r_1-72:72 atoms 12 C24__r_1-72:72 atoms 13 C25__r_1-72:72 atoms 14 C26__r_1-72:72 atoms 15 C27__r_1-72:72 atoms 16 C28__r_1-72:72 atoms And the same here - 17 groups instead of 18. I'm not familiar with the numbering, but it seems odd to jump from, e.g., C9 to C13 - are you sure your first carbon (C9) is not in the glycerol backbone rather than the ester? i'll also take a careful look into this! and the numbering is just like this. don't ask! ;) 3. What is your command for the sn-2 chain? You cannot obtain unsaturated and saturated order parameters in the same command. You must do them separately, and the index groups are different. For instance, to get the order parameters around the unsaturation, your index file should contain only Cn-1, Cn, Cn+1, Cn+2, where Cn and Cn+1 are the C atoms joined by the double bond. Then run g_order with the -unsat option. These values can then replace the corresponding carbon positions in the g_order output of the whole sn-2 chain. If done improperly, you can get weird results. the command is actually the same with the apropriate index file... maybe this is the problem for POPC - i'll look at it carefully! Then this is certainly a problem. i'll look at it with my colleague. if our problem persists, we'll get back in touch! thanks again! ^^ 4. What are the simulation conditions? Are you trying to replicate the published work? Different simulations conditions will certainly impact the structural parameters, and insufficient sampling can give weird looking curves, as well. All it might mean is that your data are not yet well-converged. NPT, surface tension of 40 dyn/cm, t=310 K, GAFF force field. the plot represents the last 10 of 150 ns of production - however, it presents the same behavior in longer (200 ns) simulations! I'd suspect the index file(s) and/or g_order commands rather than convergence issues, in this case. -Justin thanks! -Justin best regards and thanks in advance! Igor Marques -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http
Re: [gmx-users] g_membed tool
dear mohana, please refer to this page http://wwwuser.gwdg.de/%7Eggroenh/membed.html, to this article http://onlinelibrary.wiley.com/doi/10.1002/jcc.21507/pdf(g_membed: Efficient Insertion of a Membrane Protein into an Equilibrated Lipid Bilayer with Minimal Perturbation) or to this manualhttp://wwwuser.gwdg.de/%7Eggroenh/submitted/Membed_rev.pdf, that apparently compiles both the page and the article. good luck, Igor Marques On Wed, Mar 16, 2011 at 4:51 AM, Mohana lakshmi mohana...@yahoo.in wrote: Dear all.. I am using g_membed tools to embed the protein into lipid membrane. I read that before doing g_membed we need to run a short run with some options in .mdp files. what are the steps do we need to do before g_membed. It is given that box size should be taken from the membrane strucuture file but i don t know how and where to mention the size? Whether any tutorial is available for transmembrane protein using g_membed tool? Thank you Mohanalakshmi N. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] creating a bilayer of dppc
dear delara, converting the monolayer gro to pdb with editconf and then using that pdb in packmol might be a way of doing it. don't forget to adjust your *top file to the new number of items (2x) and their order. that should do it, i guess best regards, igor Igor Marques http://molecular-modeling.dq.ua.pt/ On Wed, Mar 9, 2011 at 11:16 AM, delara aghaie d_agh...@yahoo.com wrote: *Dear gromacs users* *having the .gro file for the dppc monolayer, how can i create a bilayer?* *I am interested in making bilayer from the equilibrated monolayer which i have for dppc.* *what changes are necessary to be done in simulation files to start a run with the bilayer?* *Thanks for your time* *D.M * --- On *Tue, 3/8/11, Justin A. Lemkul jalem...@vt.edu* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Instantaneous Square Displacement To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, March 8, 2011, 2:57 PM Mark Abraham wrote: On 8/03/2011 3:01 AM, Jennifer Williams wrote: Hi, I am writing a paper where I describe that gas molecules move inside a pore and then stick for long periods of time in occlusions in the pore wall. A reviewer has mentioned that I could illustrate this effect by using instantaneous square-displacement. I have already produced MSD vs time plots and used them to obtain the self diffusion coefficient. Can someone shed some light on how I can obtain the instantaneous square displacement in gromacs? I have no idea what ISD means, and Google doesn't know either :) Perhaps they want to see the diffusion of a single molecule? Searching for instantaneous square displacement turns up very little (3 results), but the last seems to be what you need, as long as this person is correct: http://smartech.gatech.edu/bitstream/handle/1853/13994/bai_xianming_200612_phd.pdf?sequence=1 Section 2.3.3. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.orghttp://us.mc1301.mail.yahoo.com/mc/compose?to=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.orghttp://us.mc1301.mail.yahoo.com/mc/compose?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] neutral plasma
Hello everybody, I've digging around the user manual, the website and the mailing list archives and I'm afraid I might be missing something: does GROMACS have some kind of *neutral plasma *as AMBER does? Or every simulation must have a net charge of 0.000 ? Best regards, Igor Marques -- 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
