Re: [gmx-users] How to use deuterium order parameters
On Wed, Nov 2, 2011 at 2:06 PM, Alex 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] lipid membrane slicing
chetan, i'm not sure about the use of -sl option in g_order. however, for the purpose you mentioned, i'd suggest you to: create two different trajectories, using trjconv and an index file grouping lipids closer to the protein and lipids away from the protein. then, you should be able to analyse each trajcetory and get the order parameters for each group of lipids. good luck, igor Igor Marques On Tue, Oct 11, 2011 at 6:20 PM, Poojari, Chetan wrote: > Hi, > > I have protein completely inserted into lipid membrane and would like to > study order parameter around the protein as well as away from the protein. > > For this I would like to slice my membrane into parts. > > I tried the following command: > > g_order -s *.tpr -f *.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -sl 2 > > The output i get from this is as same as the one where i dont use -sl 2 > flag and it also doesnt show the different parts it has used for order > parameter calculation. > > Please can I know how to slice my lipid membrane so that i can study order > parameter for each part separately. > > > Kind Regards, > chetan > > > > > > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > > > > -- > 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 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 wrote: > > > From: Justin A. Lemkul > > Subject: Re: [gmx-users] water box size from output files > > To: "Discussion list for GROMACS users" > > 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 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
thanks mate! Igor Marques On Thu, May 26, 2011 at 6:12 PM, Justin A. Lemkul 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.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" mailto:jalem...@vt.edu>> >>Subject: Re: [gmx-users] electron density >>To: Discussion list for GROMACS users ><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" ><mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> >><mailto:jalem...@vt.edu>>> >> > Subject: Re: [gmx-users] electron density >> > To: Discussion list for GROMACS users ><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 >
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 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" > Subject: Re: [gmx-users] electron density > To: Discussion list for GROMACS users > 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" mailto:jalem...@vt.edu>> > > Subject: Re: [gmx-users] electron density > > To: Discussion list for GROMACS users > <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] 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 wrote: > > Igor Marques > > > On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul wrote: > >> >> >> Igor Marques wrote: >> >> >> >> >> 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&#x
Re: [gmx-users] g_order output is mirrored
Igor Marques On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul wrote: > > > Igor Marques wrote: > > > > > 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.
Re: [gmx-users] g_order output is mirrored
Igor Marques On Tue, May 17, 2011 at 8:04 PM, Justin A. Lemkul 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 archiv
[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
<>--
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_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 manual<http://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 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 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 * wrote: > > > From: Justin A. Lemkul > Subject: Re: [gmx-users] Instantaneous Square Displacement > To: "Discussion list for GROMACS users" > 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.org<http://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.org<http://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
