Can you walk me through that image and tell me what you see that is different from what you expect? I see a maximum at z=0 in both cases (I presume z=0 is the bilayer center). I'm happy to continue guessing, but you are really best to take something like hexane in a simplified bilayer and do a test. If you don't see something like this: http://pubs.acs.org/doi/abs/10.1021/ja0535099 then you've got a problem.
________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of mahender singh <pharmbioc...@live.com> Sent: 04 May 2015 00:57 To: gromacs user_list Subject: Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4 Thanks Chris for your help I am using Isoniazid drug and the membrane model is a mixture of different lipid types (POPE,POPC,POPI,POPS,cholesterol) in a ratio mimicking the plasma membrane more closely as compared to the simple single lipid type membrane model. I have attached the PMF plot (attachment, shared link), and sorry for the partial PMF graph as one can see sampling is not sufficient , as I stopped further umbrella sampling, because of strange results. One is made by using pull-geometry=distance, free, energy on the negative side (limited to the one leaflet, as distance between two group become zero drug will not move onto the other side) and other by using pull-geometry=direction for the same drug i.e. isoniazid, free energy on the positive side. https://onedrive.live.com/redir?resid=DA38458F80BE68E9!192&authkey=!ACGecvNH6tPzIlo&ithint=folder%2c All the parameters were same except pull-geomerty i.e distance or direction. But free energy graph is completely opposite in both the cases and this should not be , as I thinks. As for the same drug free energy profile should not be completely opposite for the one drug, so may be I making some mistake in the umbrella sampling parameters. Can you provide me some suggestion on this topic. Thanks in advance for help. with regards Mahender Singh > Hello > good morning to all > > I did steered md simulation by using following code > ;pull code > pull = umbrella > pull_geometry = direction > pull_dim = N N Y > pull_coord1_vec =0 0 1 > pull_start = yes > pull_ngroups =2 > pull-ncoords =1 > pull_coord1_groups = 1 2 > pull_group1_name = NPROT_ref > pull_group2_name = LIG > pull_coord1_rate = 0.004 ; 0.004 nm per ps = 4 nm per ns > pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 > pull_nstxout = 500 ; every 1 ps > pull_nstfout = 500 ; every 1 ps > > And then used these results of SMD for umbrella sampling (total umbrella > window =30 across the membrane) by using following code > > pull = umbrella > pull_geometry = direction > pull_dim = N N Y > pull_coord1_vec =0 0 1 > pull_start = yes > pull_ngroups =2 > pull-ncoords =1 > pull_coord1_groups = 1 2 > pull_group1_name = NPROT_ref > pull_group2_name = LIG > pull_coord1_rate = 0.0 > pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 > pull_nstxout = 500 ; every 1 ps > pull_nstfout = 500 ; every 1 ps > > In my case, I am moving a molecule from -z to +z across the membrane. So I > used pull-geometry=direction in gromacs 5.0.4 (as per gromacs site= > http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force), as I > cannot use pull-geimetry=distance. Every thing completed correctly (seems to > me), but when I used gmx wham on the pullf.xvg files, PMF profile was on the > positive side. PMF increased from 0 (bulk water) to 60 at the center of the > membrane and than again decreased to the 0 (bulk water on the other side). > I all the literature, PMF values for the molecule crossing a membrane is on > the negative side and minimum at the center. > I am confused about the result. Did I do something wrong with the parameters > or understanding the PMF curve wrongly. > > can any one give their suggestion on this. > > thanks in advance of user time and help. > > with regards > Mahender Singh > > -- > 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. > > > ------------------------------ > > Message: 3 > Date: Sun, 3 May 2015 12:25:01 +0000 > From: Christopher Neale <chris.ne...@alum.utoronto.ca> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] umbrella sampling and PMF calculation by > using pull-geometry=direction in gromacs 5.0.4 > Message-ID: <1430655898617.32...@alum.utoronto.ca> > Content-Type: text/plain; charset="iso-8859-1" > > Better yet, repeat something that is already out there in the literature. > PMFs for water, lipids, and some amino acid side chains across the bilayer > have been tested extensively. > > Chris. > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of mahender > singh <pharmbioc...@live.com> > Sent: 03 May 2015 01:07 > To: gromacs user_list > Subject: [gmx-users] umbrella sampling and PMF calculation by using > pull-geometry=direction in gromacs 5.0.4 > > Hello > good morning to all > > I did steered md simulation by using following code > ;pull code > pull = umbrella > pull_geometry = direction > pull_dim = N N Y > pull_coord1_vec =0 0 1 > pull_start = yes > pull_ngroups =2 > pull-ncoords =1 > pull_coord1_groups = 1 2 > pull_group1_name = NPROT_ref > pull_group2_name = LIG > pull_coord1_rate = 0.004 ; 0.004 nm per ps = 4 nm per ns > pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 > pull_nstxout = 500 ; every 1 ps > pull_nstfout = 500 ; every 1 ps > > And then used these results of SMD for umbrella sampling (total umbrella > window =30 across the membrane) by using following code > > pull = umbrella > pull_geometry = direction > pull_dim = N N Y > pull_coord1_vec =0 0 1 > pull_start = yes > pull_ngroups =2 > pull-ncoords =1 > pull_coord1_groups = 1 2 > pull_group1_name = NPROT_ref > pull_group2_name = LIG > pull_coord1_rate = 0.0 > pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 > pull_nstxout = 500 ; every 1 ps > pull_nstfout = 500 ; every 1 ps > > In my case, I am moving a molecule from -z to +z across the membrane. So I > used pull-geometry=direction in gromacs 5.0.4 (as per gromacs site= > http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force), as I > cannot use pull-geimetry=distance. Every thing completed correctly (seems to > me), but when I used gmx wham on the pullf.xvg files, PMF profile was on the > positive side. PMF increased from 0 (bulk water) to 60 at the center of the > membrane and than again decreased to the 0 (bulk water on the other side). > I all the literature, PMF values for the molecule crossing a membrane is on > the negative side and minimum at the center. > I am confused about the result. Did I do something wrong with the parameters > or understanding the PMF curve wrongly. > > can any one give their suggestion on this. > > thanks in advance of user time and help. > > with regards > Mahender Singh > > -- > 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. > > > ------------------------------ > > Message: 4 > Date: Mon, 4 May 2015 01:07:16 +1200 > From: James Lord <jjamesgreen...@gmail.com> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>, Justin Lemkul > <jalem...@vt.edu> > Subject: Re: [gmx-users] Justin biphasic tutorial with controlled > adsoption of protein > Message-ID: > <caauhnntfbtgw92t_c98fqkhvwycdt453jva_1wr1fdm4mf1...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Justin, > Thanks for the info, your assumption re long axis of the box is correct > (z), here is the .gro file I have for one the oil (decane)-protein (the > protein is in the middle part of the free space above the oil surface). Is > that what you were talking about? I went through manual and could not get > what to do for position restrains, appreciate if you can elaborate further > on it? Thanks for your final point re solvent/ions separate coupling. > https://drive.google.com/file/d/0B0YMTXH1gmQsYmQzRXUtN1ZENmc/view?usp=sharing > Cheers > James > > > On Sun, May 3, 2015 at 4:23 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 5/2/15 10:02 AM, James Lord wrote: > > > >> Dear gmx users, > >> I have a biphasic system, like Justin's tutorial, but I want to control > >> the protein to adsorb/desorb from the oil-water interface, I don't want > >> the > >> protein to go through oil phase just want to keep it at the interface, I > >> have added a constant force at the end of the mdp file. i tried different > >> pull_k1 values but what I see is, when the force is applied the oil is > >> also > >> deformed (which makes sense) and kinda make a hole in the oil phase and > >> eventually pass through it. I just want to keep it at or away from the > >> interface without deforming/puling away the oil molecules, What is the > >> best > >> way to do it? any suggestion? here is the mdp > >> https://drive.google.com/open?id=0B0YMTXH1gmQsZ1ljOUZROWNGM3M&authuser=0 > >> > >> > > I wouldn't use the pull code. This sounds like a task best suited for a > > flat-bottom restraint. I'm going to assume the long axis of the box is > > along z for this example. You can create a coordinate file in which the > > z-coordinate of all the protein atoms is equal to the middle of the box > > (this assumes the z dimension of the box doesn't change, e.g. semiisotropic > > pressure coupling with compressibility of zero along z). Then supply this > > file to grompp -r with a suitable [position_restraints] section that > > specifies a flat-bottom potential along z (see manual section 4.3.2, I > > think this is a case where you need a negative force constant to keep the > > atoms "outside" of the restraint region). During the run, if any protein > > atom hits the imaginary wall, it gets pushed back in the other direction by > > the flat-bottom restraint. > > > > Also, don't couple solvent and ions to separate thermostats. It's not > > sensible and usually not stable. > > > > -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. > > > > > ------------------------------ > > Message: 5 > Date: Sun, 3 May 2015 11:57:56 -0400 > From: shivangi nangia <shivangi.nan...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org>, Tsjerk > Wassenaar <tsje...@gmail.com> > Subject: Re: [gmx-users] Secondary Structure Restraints: martinize.py > Message-ID: > <CAH137_+=1v94zhqp2lasqvd84oia169s_sgjt+8oeufldhn...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hello Tsjerk, > > > I am executing the following command to get half helical and half random cg > structure > > The pdb I am supplying is a helical peptide > > ./martinize.py -f gamma1_unmutated.pdb -x gamma1_unmutated.elnedyn.pdb -o > gamma1.elnedyn.top -ss LLLLLLLLLLHHHHHHHHHHH -p backbone -ff martini22 > > martinize.out > > Then I minimize and rebox this cg peptide and reverse cg > > ./my_intiram.sh -f ../elnedynoff/reboxed_min_gamma1.gro -p protein_aa.top > -po prot_bkmapped.top -from martini -to charmm36 > > The backmapped.gro I get is not half random/half helical. > > Is there anything that I am doing wrong? > > Kindly guide. > > Thanks, > sxn > > On Fri, May 1, 2015 at 4:43 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > > Hi sxn, > > > > With martinize.py -ss LLLLLLLLLLLHHHHHHHHHH > > you'll get the secondary structure you want. > > > > Cheers, > > > > Tsjerk > > > > On Fri, May 1, 2015 at 10:24 PM, shivangi nangia < > > shivangi.nan...@gmail.com> > > wrote: > > > > > Hello Tsjerk, > > > > > > Thanks for the reply. > > > > > > I have a 21 amino acids helical peptide, I want to first 10 amino acids > > to > > > not having secondary structure restraints while coarse graining using > > > martinize.py and the rest to remain helical. > > > > > > I reverse coarse the peptide to see if my trials while playing around > > with > > > different trials with secondary structure file (I provide with -ss) > > changes > > > worked or not. For example, in one of my trials I changed the structure > > > column of the .dssp file from H to nothing hoping once I coarse grain > > with > > > that modified file I would get a semi secondary structure restrained > > coarse > > > grained peptide. > > > > > > Thanks, > > > > > > sxn > > > > > > On Fri, May 1, 2015 at 3:59 PM, Tsjerk Wassenaar <tsje...@gmail.com> > > > wrote: > > > > > > > Hi sxn, > > > > > > > > What do you mean with reverse coarse graining? > > > > You can specify the secondary structure also as string, which is doable > > > if > > > > the peptide is not too long, e.g. using -ss HHHHHHHLLLLLLL. Otherwise, > > > you > > > > can put the secondary structure you want in a simple file, and pass > > that > > > > with the option -ss. > > > > > > > > Cheers, > > > > > > > > Tsjerk > > > > > > > > > > > > On Fri, May 1, 2015 at 4:24 PM, shivangi nangia < > > > shivangi.nan...@gmail.com > > > > > > > > > wrote: > > > > > > > > > Hello, > > > > > > > > > > I wish to turn off the secondary structure restraint in half of the > > > > peptide > > > > > while using martinze.py. > > > > > > > > > > Is there any way in which this can be done. > > > > > > > > > > I have tried to delete the columns in .dssp file which tell about the > > > > > structure and character of the peptide but I still get a completely > > > > helical > > > > > peptide on reverse coarse graining. > > > > > > > > > > Thanks in advance. > > > > > > > > > > Best, > > > > > sxn > > > > > -- > > > > > 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. > > > > > > > > > > > > > > > > > > > > > -- > > > > Tsjerk A. Wassenaar, Ph.D. > > > > -- > > > > 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. > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > 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? 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