[gmx-users] Coulomb values
Dear Gromacs users, I was trying to extract electrostatics and van der Waals interactions for specific lipid molecules in the system I simulated. I assume you can get the coulomb and LJ values from energy. But why is there more than one options to select for both Coulomb and LJ from the list.? Thanks Merril. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Surface tension/pressure calculation
Dear all, I would like to calculate surface tension/pressure of my monolayer simulation. I have two monolayers of lipid each side of a water box. So four interfaces; vaccum/lipid, lipid/water, water/lipid and lipid/vaccum. I used NVT simulation. Is there a way to calculate surface tension/pressure of lipid/water in my system using GROMACS tools? I used: gmx energy to get #Surf*SurfTens. What does this do? Is it possible to calculate the surface tension of my monolayers using the formula: [image: Inline images 1] I can get Pzz, Pxx and Pyy for my system from gmx_energy. Is Lz the box size in Z direction, i.e normal to my monolayer in nanometers? If I solve this equation does the value mean the average surface tension of my monolayers? Thanks, Merril. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Lipid head movement normal to monolayer.
Thanks Catarina. On 16 Mar 2017 10:53 a.m., "Catarina A. Carvalheda dos Santos" < c.a.c.dossan...@dundee.ac.uk> wrote: > Hey, > > I'm not sure about lipid headgroups "emersing" "into water". Maybe > calculate the average and individual positions of the P and/or N atoms in > the z axis for each frame. It's normal that there are some fluctuations > though. > > Anyways, if you want to compare the movement of each lipid molecule in > relation to the initial configuration I guess you can use g_rms (and use > the initial conformation as reference). > > Hope this helps. > > Regards, > > On 15 March 2017 at 21:28, Merril Mathew wrote: > > > Dear all, > > > > I want to calculate how much my lipid heads emerse into water in a > > monolayer after simulation. I want to compare the movement of the lipids > > from the intial conformation to the final conformation. Is there a way to > > calculate such movement using GROMACS? > > > > Merril. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > > > > > -- > Catarina A. Carvalheda > > PhD Student > Computational Biology Division > SLS & SSE > University of Dundee > DD1 5EH, Dundee, Scotland, UK > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Lipid head movement normal to monolayer.
Dear all, I want to calculate how much my lipid heads emerse into water in a monolayer after simulation. I want to compare the movement of the lipids from the intial conformation to the final conformation. Is there a way to calculate such movement using GROMACS? Merril. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Order parameter for double bonded lipids
Is the modified parameter file for POPG from your work available online? Merril. On 10 Mar 2017 7:05 a.m., "Merril Mathew" wrote: > many thanks Tom. > > On 10 Mar 2017 1:35 a.m., "Thomas Piggot" wrote: > >> So this isn't a berger based PG rather a pure GROMOS one. But yes, it >> also has problems. The double bond dihedrals don't work well and so you get >> really poor order parameters after the double bond (see >> http://pubs.acs.org/doi/abs/10.1021/ct3003157 for POPC but the same is >> true of POPG). From what I remember, this itp also has extraneous dihedrals >> in the glycerol regions plus some other issues with the bonded parameters ( >> http://pubs.acs.org/doi/suppl/10.1021/jp207013v) but I cannot remember >> off the top of my head the impact they made. >> >> Up to you to decide with the density calculation. >> >> Cheers >> >> Tom >> >> On 10/03/17 00:45, Merril Mathew wrote: >> >>> The POPG .itp and .pdb files were obtained from, >>> https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html >>> Author : A Kukol. >>> I used D-POPG. Should I use electron density or mass for calculating >>> monolayer thickness? >>> >>> Merril. >>> >>> On 10 Mar 2017 00:36, "Thomas Piggot" wrote: >>> >>> How did you get/make the itp for POPG, this isn't available from the >>>> Tieleman group website. The Berger parameters don't work well for PG. >>>> For >>>> example, you will see ring like structures in the head group if you >>>> look at >>>> the simulations in something like VMD. The APL for bilayers (and I >>>> imagine >>>> monolayers) will also be too low. You can find more details in >>>> http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore >>>> models >>>> are Berger based ones). >>>> >>>> For the APL, the calculation is trivial using the box vectors (from gmx >>>> energy or gmx traj). For the thickness, you can probably use gmx >>>> density to >>>> create a density profile of your monolayer and work out a thickness from >>>> that. >>>> >>>> Tom >>>> >>>> On 10/03/17 00:24, Merril Mathew wrote: >>>> >>>> I am using Berger lipid from Dr.Tielemens website and modified the >>>>> gromos >>>>> forcefield to include the lipid parameters. Out of interest, Do you >>>>> know >>>>> any gromacs tools or other programs that calculatg the area per lipid >>>>> and >>>>> bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM >>>>> but >>>>> it only works with bilyer lipids. thanks. >>>>> >>>>> Merril. >>>>> >>>>> On 10 Mar 2017 00:19, "Thomas Piggot" wrote: >>>>> >>>>> Sort of. The saturated carbons after the double bond will be correct >>>>> too, >>>>> >>>>>> just not C9 and C10 in the double bond (as you need different >>>>>> assumptions >>>>>> for calculating these in united-atom system which the -unsat option is >>>>>> meant to do correctly but doesn't). Additionally, there are tools out >>>>>> there >>>>>> that will work for calculating the order parameters of the unsaturated >>>>>> bond >>>>>> if you need it. >>>>>> >>>>>> GROMOS 53A6 is not really a lipid force field per say but there are PG >>>>>> compatible lipids (Kukol, different Berger variants, GROMOS-CKP). >>>>>> Which >>>>>> lipid parameters are you using? Lots of them don't work well at all. >>>>>> >>>>>> Cheers >>>>>> >>>>>> Tom >>>>>> >>>>>> On 10/03/17 00:10, Merril Mathew wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>>> I am using a united atom forcefield. gromos53a6. So does that mean as >>>>>>> long >>>>>>> as I avoid the double bond and the subsequent carbons after the >>>>>>> double >>>>>>> bond, then the calculation is correct? I understand it does not >>>>>>> describe >>>>>>> the full lipid length but can be used to
Re: [gmx-users] Order parameter for double bonded lipids
many thanks Tom. On 10 Mar 2017 1:35 a.m., "Thomas Piggot" wrote: > So this isn't a berger based PG rather a pure GROMOS one. But yes, it also > has problems. The double bond dihedrals don't work well and so you get > really poor order parameters after the double bond (see > http://pubs.acs.org/doi/abs/10.1021/ct3003157 for POPC but the same is > true of POPG). From what I remember, this itp also has extraneous dihedrals > in the glycerol regions plus some other issues with the bonded parameters ( > http://pubs.acs.org/doi/suppl/10.1021/jp207013v) but I cannot remember > off the top of my head the impact they made. > > Up to you to decide with the density calculation. > > Cheers > > Tom > > On 10/03/17 00:45, Merril Mathew wrote: > >> The POPG .itp and .pdb files were obtained from, >> https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html >> Author : A Kukol. >> I used D-POPG. Should I use electron density or mass for calculating >> monolayer thickness? >> >> Merril. >> >> On 10 Mar 2017 00:36, "Thomas Piggot" wrote: >> >> How did you get/make the itp for POPG, this isn't available from the >>> Tieleman group website. The Berger parameters don't work well for PG. For >>> example, you will see ring like structures in the head group if you look >>> at >>> the simulations in something like VMD. The APL for bilayers (and I >>> imagine >>> monolayers) will also be too low. You can find more details in >>> http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore >>> models >>> are Berger based ones). >>> >>> For the APL, the calculation is trivial using the box vectors (from gmx >>> energy or gmx traj). For the thickness, you can probably use gmx density >>> to >>> create a density profile of your monolayer and work out a thickness from >>> that. >>> >>> Tom >>> >>> On 10/03/17 00:24, Merril Mathew wrote: >>> >>> I am using Berger lipid from Dr.Tielemens website and modified the gromos >>>> forcefield to include the lipid parameters. Out of interest, Do you know >>>> any gromacs tools or other programs that calculatg the area per lipid >>>> and >>>> bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM >>>> but >>>> it only works with bilyer lipids. thanks. >>>> >>>> Merril. >>>> >>>> On 10 Mar 2017 00:19, "Thomas Piggot" wrote: >>>> >>>> Sort of. The saturated carbons after the double bond will be correct >>>> too, >>>> >>>>> just not C9 and C10 in the double bond (as you need different >>>>> assumptions >>>>> for calculating these in united-atom system which the -unsat option is >>>>> meant to do correctly but doesn't). Additionally, there are tools out >>>>> there >>>>> that will work for calculating the order parameters of the unsaturated >>>>> bond >>>>> if you need it. >>>>> >>>>> GROMOS 53A6 is not really a lipid force field per say but there are PG >>>>> compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which >>>>> lipid parameters are you using? Lots of them don't work well at all. >>>>> >>>>> Cheers >>>>> >>>>> Tom >>>>> >>>>> On 10/03/17 00:10, Merril Mathew wrote: >>>>> >>>>> Hi, >>>>> >>>>>> I am using a united atom forcefield. gromos53a6. So does that mean as >>>>>> long >>>>>> as I avoid the double bond and the subsequent carbons after the double >>>>>> bond, then the calculation is correct? I understand it does not >>>>>> describe >>>>>> the full lipid length but can be used to assess the monolayer >>>>>> behaviour >>>>>> roughly. >>>>>> >>>>>> Merril. >>>>>> >>>>>> On 10 Mar 2017 12:04 a.m., "Thomas Piggot" >>>>>> wrote: >>>>>> >>>>>> The order parameters calculated for all the saturated carbons will be >>>>>> >>>>>> correct but the gmx order program doesn't calculate the order >>>>>>> parameters >>>>>>> for the unsaturated carbons correctly (even wh
Re: [gmx-users] Calculating area per lipid and monolayer thickness
thanks Justin. On 8 Mar 2017 13:09, "Justin Lemkul" wrote: > > > On 3/8/17 8:06 AM, Merril Mathew wrote: > >> I dont know what I am doing wrong. There is no Box-X or Box-Y when >> prompted. These are the list I get: >> - >> 1 Angle2 Proper-Dih. 3 Ryckaert-Bell. 4 >> Improper-Dih. >> 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 >> Disper.-corr. >> 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 >> Kinetic-En. >> 13 Total-Energy14 Conserved-En. 15 Temperature 16 >> Pres.-DC >> 17 Pressure18 Constr.-rmsd19 Vir-XX 20 >> Vir-XY >> 21 Vir-XZ 22 Vir-YX 23 Vir-YY 24 >> Vir-YZ >> 25 Vir-ZX 26 Vir-ZY 27 Vir-ZZ 28 >> Pres-XX >> 29 Pres-XY 30 Pres-XZ 31 Pres-YX 32 >> Pres-YY >> 33 Pres-YZ 34 Pres-ZX 35 Pres-ZY 36 >> Pres-ZZ >> 37 #Surf*SurfTen 38 T-DPOPG_OPO 39 T-SOL_Ion >> >> 38 and 39 are the coupling groups I used. >> > > If there is no option to select box vectors, then your simulation was NVT > and by definition the box vectors don't vary and your membrane area is > constant. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Order parameter for double bonded lipids
I also used the same POPG .itp and .pdb files to edit and create an oxidised version of the molecule with aldehyde group replacing the double bond. Is there a problem associated with parameters from A Kukol for POPG? On 10 Mar 2017 00:45, "Merril Mathew" wrote: > The POPG .itp and .pdb files were obtained from, > https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html > Author : A Kukol. > I used D-POPG. Should I use electron density or mass for calculating > monolayer thickness? > > Merril. > > On 10 Mar 2017 00:36, "Thomas Piggot" wrote: > >> How did you get/make the itp for POPG, this isn't available from the >> Tieleman group website. The Berger parameters don't work well for PG. For >> example, you will see ring like structures in the head group if you look at >> the simulations in something like VMD. The APL for bilayers (and I imagine >> monolayers) will also be too low. You can find more details in >> http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore >> models are Berger based ones). >> >> For the APL, the calculation is trivial using the box vectors (from gmx >> energy or gmx traj). For the thickness, you can probably use gmx density to >> create a density profile of your monolayer and work out a thickness from >> that. >> >> Tom >> >> On 10/03/17 00:24, Merril Mathew wrote: >> >>> I am using Berger lipid from Dr.Tielemens website and modified the gromos >>> forcefield to include the lipid parameters. Out of interest, Do you know >>> any gromacs tools or other programs that calculatg the area per lipid and >>> bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM >>> but >>> it only works with bilyer lipids. thanks. >>> >>> Merril. >>> >>> On 10 Mar 2017 00:19, "Thomas Piggot" wrote: >>> >>> Sort of. The saturated carbons after the double bond will be correct too, >>>> just not C9 and C10 in the double bond (as you need different >>>> assumptions >>>> for calculating these in united-atom system which the -unsat option is >>>> meant to do correctly but doesn't). Additionally, there are tools out >>>> there >>>> that will work for calculating the order parameters of the unsaturated >>>> bond >>>> if you need it. >>>> >>>> GROMOS 53A6 is not really a lipid force field per say but there are PG >>>> compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which >>>> lipid parameters are you using? Lots of them don't work well at all. >>>> >>>> Cheers >>>> >>>> Tom >>>> >>>> On 10/03/17 00:10, Merril Mathew wrote: >>>> >>>> Hi, >>>>> >>>>> I am using a united atom forcefield. gromos53a6. So does that mean as >>>>> long >>>>> as I avoid the double bond and the subsequent carbons after the double >>>>> bond, then the calculation is correct? I understand it does not >>>>> describe >>>>> the full lipid length but can be used to assess the monolayer behaviour >>>>> roughly. >>>>> >>>>> Merril. >>>>> >>>>> On 10 Mar 2017 12:04 a.m., "Thomas Piggot" >>>>> wrote: >>>>> >>>>> The order parameters calculated for all the saturated carbons will be >>>>> >>>>>> correct but the gmx order program doesn't calculate the order >>>>>> parameters >>>>>> for the unsaturated carbons correctly (even when using the -unsat >>>>>> option). >>>>>> >>>>>> Out of interest, is this a united-atom or all-atom force field you are >>>>>> using? >>>>>> >>>>>> Cheers >>>>>> >>>>>> Tom >>>>>> >>>>>> On 09/03/17 23:51, Merril Mathew wrote: >>>>>> >>>>>> Hi, >>>>>> >>>>>>> I followed turorials found on Bevanlab by Justin. I successfully >>>>>>> calculated >>>>>>> order parameter for DPPC molecules in my system following the >>>>>>> tutorial. >>>>>>> My >>>>>>> question is whether the same calculation can be applied for a POPG >>>>>>> molecule >>>>>>> with a double bond
Re: [gmx-users] Order parameter for double bonded lipids
The POPG .itp and .pdb files were obtained from, https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html Author : A Kukol. I used D-POPG. Should I use electron density or mass for calculating monolayer thickness? Merril. On 10 Mar 2017 00:36, "Thomas Piggot" wrote: > How did you get/make the itp for POPG, this isn't available from the > Tieleman group website. The Berger parameters don't work well for PG. For > example, you will see ring like structures in the head group if you look at > the simulations in something like VMD. The APL for bilayers (and I imagine > monolayers) will also be too low. You can find more details in > http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore models > are Berger based ones). > > For the APL, the calculation is trivial using the box vectors (from gmx > energy or gmx traj). For the thickness, you can probably use gmx density to > create a density profile of your monolayer and work out a thickness from > that. > > Tom > > On 10/03/17 00:24, Merril Mathew wrote: > >> I am using Berger lipid from Dr.Tielemens website and modified the gromos >> forcefield to include the lipid parameters. Out of interest, Do you know >> any gromacs tools or other programs that calculatg the area per lipid and >> bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM >> but >> it only works with bilyer lipids. thanks. >> >> Merril. >> >> On 10 Mar 2017 00:19, "Thomas Piggot" wrote: >> >> Sort of. The saturated carbons after the double bond will be correct too, >>> just not C9 and C10 in the double bond (as you need different assumptions >>> for calculating these in united-atom system which the -unsat option is >>> meant to do correctly but doesn't). Additionally, there are tools out >>> there >>> that will work for calculating the order parameters of the unsaturated >>> bond >>> if you need it. >>> >>> GROMOS 53A6 is not really a lipid force field per say but there are PG >>> compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which >>> lipid parameters are you using? Lots of them don't work well at all. >>> >>> Cheers >>> >>> Tom >>> >>> On 10/03/17 00:10, Merril Mathew wrote: >>> >>> Hi, >>>> >>>> I am using a united atom forcefield. gromos53a6. So does that mean as >>>> long >>>> as I avoid the double bond and the subsequent carbons after the double >>>> bond, then the calculation is correct? I understand it does not >>>> describe >>>> the full lipid length but can be used to assess the monolayer behaviour >>>> roughly. >>>> >>>> Merril. >>>> >>>> On 10 Mar 2017 12:04 a.m., "Thomas Piggot" >>>> wrote: >>>> >>>> The order parameters calculated for all the saturated carbons will be >>>> >>>>> correct but the gmx order program doesn't calculate the order >>>>> parameters >>>>> for the unsaturated carbons correctly (even when using the -unsat >>>>> option). >>>>> >>>>> Out of interest, is this a united-atom or all-atom force field you are >>>>> using? >>>>> >>>>> Cheers >>>>> >>>>> Tom >>>>> >>>>> On 09/03/17 23:51, Merril Mathew wrote: >>>>> >>>>> Hi, >>>>> >>>>>> I followed turorials found on Bevanlab by Justin. I successfully >>>>>> calculated >>>>>> order parameter for DPPC molecules in my system following the >>>>>> tutorial. >>>>>> My >>>>>> question is whether the same calculation can be applied for a POPG >>>>>> molecule >>>>>> with a double bond in the acyl chain.? can I group all the carbon upto >>>>>> the >>>>>> double bond, therefore ignoring the double bond and the rest of the >>>>>> carbons >>>>>> in the chain to calculate order parameter? Is that a reasonable >>>>>> analysis >>>>>> to >>>>>> measure the order of POPG molecules.? Thanks. >>>>>> >>>>>> -- >>>>>> >>>>> Dr Thomas Piggot >>>>> Visiting Fellow >>>>> University of Southampton, UK. >>>>> >>>>> -- >>>&g
Re: [gmx-users] Order parameter for double bonded lipids
I am using Berger lipid from Dr.Tielemens website and modified the gromos forcefield to include the lipid parameters. Out of interest, Do you know any gromacs tools or other programs that calculatg the area per lipid and bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM but it only works with bilyer lipids. thanks. Merril. On 10 Mar 2017 00:19, "Thomas Piggot" wrote: > Sort of. The saturated carbons after the double bond will be correct too, > just not C9 and C10 in the double bond (as you need different assumptions > for calculating these in united-atom system which the -unsat option is > meant to do correctly but doesn't). Additionally, there are tools out there > that will work for calculating the order parameters of the unsaturated bond > if you need it. > > GROMOS 53A6 is not really a lipid force field per say but there are PG > compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which > lipid parameters are you using? Lots of them don't work well at all. > > Cheers > > Tom > > On 10/03/17 00:10, Merril Mathew wrote: > >> Hi, >> >> I am using a united atom forcefield. gromos53a6. So does that mean as long >> as I avoid the double bond and the subsequent carbons after the double >> bond, then the calculation is correct? I understand it does not describe >> the full lipid length but can be used to assess the monolayer behaviour >> roughly. >> >> Merril. >> >> On 10 Mar 2017 12:04 a.m., "Thomas Piggot" wrote: >> >> The order parameters calculated for all the saturated carbons will be >>> correct but the gmx order program doesn't calculate the order parameters >>> for the unsaturated carbons correctly (even when using the -unsat >>> option). >>> >>> Out of interest, is this a united-atom or all-atom force field you are >>> using? >>> >>> Cheers >>> >>> Tom >>> >>> On 09/03/17 23:51, Merril Mathew wrote: >>> >>> Hi, >>>> >>>> I followed turorials found on Bevanlab by Justin. I successfully >>>> calculated >>>> order parameter for DPPC molecules in my system following the tutorial. >>>> My >>>> question is whether the same calculation can be applied for a POPG >>>> molecule >>>> with a double bond in the acyl chain.? can I group all the carbon upto >>>> the >>>> double bond, therefore ignoring the double bond and the rest of the >>>> carbons >>>> in the chain to calculate order parameter? Is that a reasonable analysis >>>> to >>>> measure the order of POPG molecules.? Thanks. >>>> >>>> -- >>> Dr Thomas Piggot >>> Visiting Fellow >>> University of Southampton, UK. >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > Dr Thomas Piggot > Visiting Fellow > University of Southampton, UK. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Order parameter for double bonded lipids
Hi, I am using a united atom forcefield. gromos53a6. So does that mean as long as I avoid the double bond and the subsequent carbons after the double bond, then the calculation is correct? I understand it does not describe the full lipid length but can be used to assess the monolayer behaviour roughly. Merril. On 10 Mar 2017 12:04 a.m., "Thomas Piggot" wrote: > The order parameters calculated for all the saturated carbons will be > correct but the gmx order program doesn't calculate the order parameters > for the unsaturated carbons correctly (even when using the -unsat option). > > Out of interest, is this a united-atom or all-atom force field you are > using? > > Cheers > > Tom > > On 09/03/17 23:51, Merril Mathew wrote: > >> Hi, >> >> I followed turorials found on Bevanlab by Justin. I successfully >> calculated >> order parameter for DPPC molecules in my system following the tutorial. My >> question is whether the same calculation can be applied for a POPG >> molecule >> with a double bond in the acyl chain.? can I group all the carbon upto the >> double bond, therefore ignoring the double bond and the rest of the >> carbons >> in the chain to calculate order parameter? Is that a reasonable analysis >> to >> measure the order of POPG molecules.? Thanks. >> > > -- > Dr Thomas Piggot > Visiting Fellow > University of Southampton, UK. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Order parameter for double bonded lipids
Hi, I followed turorials found on Bevanlab by Justin. I successfully calculated order parameter for DPPC molecules in my system following the tutorial. My question is whether the same calculation can be applied for a POPG molecule with a double bond in the acyl chain.? can I group all the carbon upto the double bond, therefore ignoring the double bond and the rest of the carbons in the chain to calculate order parameter? Is that a reasonable analysis to measure the order of POPG molecules.? Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Calculating area per lipid and monolayer thickness
I dont know what I am doing wrong. There is no Box-X or Box-Y when prompted. These are the list I get: - 1 Angle2 Proper-Dih. 3 Ryckaert-Bell. 4 Improper-Dih. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 Disper.-corr. 9 Coulomb-(SR)10 Coul.-recip.11 Potential 12 Kinetic-En. 13 Total-Energy14 Conserved-En. 15 Temperature 16 Pres.-DC 17 Pressure18 Constr.-rmsd19 Vir-XX 20 Vir-XY 21 Vir-XZ 22 Vir-YX 23 Vir-YY 24 Vir-YZ 25 Vir-ZX 26 Vir-ZY 27 Vir-ZZ 28 Pres-XX 29 Pres-XY 30 Pres-XZ 31 Pres-YX 32 Pres-YY 33 Pres-YZ 34 Pres-ZX 35 Pres-ZY 36 Pres-ZZ 37 #Surf*SurfTen 38 T-DPOPG_OPO 39 T-SOL_Ion 38 and 39 are the coupling groups I used. Merril. On 8 March 2017 at 12:56, Justin Lemkul wrote: > > > On 3/8/17 7:52 AM, Merril Mathew wrote: > >> I am not sure what command to use to extract the X and Y box vector. is it >> gmx energy -f md.edr -o .xvg? >> > > Yes. > > and which option should I choose from the list? >> >> > The ones I said before, (the aptly named) Box-X and Box-Y. > > -Justin > > > On 8 Mar 2017 12:44 p.m., "Justin Lemkul" wrote: >> >> >>> >>> On 3/8/17 7:28 AM, Merril Mathew wrote: >>> >>> I have a system that I simulated using GROMACS v5.0.4. The system is two >>>> monolayers of lipid on each side of a box of water. I would like to know >>>> if >>>> there is a way to calculate area per lipid and monolayer thickness. I >>>> read >>>> that one can use gmx energy to find box size in X and Y and you divide >>>> the >>>> average time evolution box size( X*Y) by number of lipids. >>>> >>>> I used commmand: >>>> gmx energy -f md.edr -s md.tpr -o box_vector.xvg >>>> >>>> What option should I select when prompted to get X and Y box >>>> dimensions.? >>>> How is the box vector calculated? I have noticed that the lipids pack >>>> closely after simulation, that means the the area per lipid will be >>>> smaller >>>> than the initial configuration file. So does the box X and Y get smaller >>>> as >>>> well? >>>> >>>> >>>> What you want are Box-X and Box-Y from the .edr file. Then you can see >>> the time series of how the box size changes. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Calculating area per lipid and monolayer thickness
I am not sure what command to use to extract the X and Y box vector. is it gmx energy -f md.edr -o .xvg? and which option should I choose from the list? On 8 Mar 2017 12:44 p.m., "Justin Lemkul" wrote: > > > On 3/8/17 7:28 AM, Merril Mathew wrote: > >> I have a system that I simulated using GROMACS v5.0.4. The system is two >> monolayers of lipid on each side of a box of water. I would like to know >> if >> there is a way to calculate area per lipid and monolayer thickness. I read >> that one can use gmx energy to find box size in X and Y and you divide the >> average time evolution box size( X*Y) by number of lipids. >> >> I used commmand: >> gmx energy -f md.edr -s md.tpr -o box_vector.xvg >> >> What option should I select when prompted to get X and Y box dimensions.? >> How is the box vector calculated? I have noticed that the lipids pack >> closely after simulation, that means the the area per lipid will be >> smaller >> than the initial configuration file. So does the box X and Y get smaller >> as >> well? >> >> > What you want are Box-X and Box-Y from the .edr file. Then you can see > the time series of how the box size changes. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Calculating area per lipid and monolayer thickness
I have a system that I simulated using GROMACS v5.0.4. The system is two monolayers of lipid on each side of a box of water. I would like to know if there is a way to calculate area per lipid and monolayer thickness. I read that one can use gmx energy to find box size in X and Y and you divide the average time evolution box size( X*Y) by number of lipids. I used commmand: gmx energy -f md.edr -s md.tpr -o box_vector.xvg What option should I select when prompted to get X and Y box dimensions.? How is the box vector calculated? I have noticed that the lipids pack closely after simulation, that means the the area per lipid will be smaller than the initial configuration file. So does the box X and Y get smaller as well? Merril. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
