[gmx-users] solvent orientation/sorient
I want to calculate solvent orientation around two types of spherical particle. The solvent has a long alkyl chain. I use sorient with three atoms in the carbon chain in my index group, one at each end and one in the middle. The results are confusing me. Theta_1 is described as "the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3". Therefore (it seems to me), if the alkyl chain is mostly sticking out perpendicular from the surface of the spherical particle, theta_1 should be close to 0 and cos(theta_1) should be close to 1. If the alkyl chain is more wrapped around the spherical particle, parallel to the surface, theta_1 should be closer to 90 degrees and cos(theta_1) should be closer to 0. However, when I examine the two types of spherical particles visually and compare them to the results from sorient, it seems to be the opposite--the system where the alkyl chain looks (visually) more perpendicular to the particle surface has lower cos(theta_1). Am I misunderstanding which angle exactly theta_1 is or should I just trust the sorient calculation over what appears to me visually? -- 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] LJ-SR and LJ-14
If you want the "total" Lennard-Jones potential between two groups, would you simply add LJ-SR + LJ-14? If so, what is the utility of calculating both potentials separately? -- 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] Pull Code Error "unknown left hand"
I am attempting to pull a particle across a simulation box. I did it several times with version 4.6.3 but this is my first attempting to do it with version 5.0.4. I modified my mdp file for the new version based on the updated tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html). My pull code looks like this: ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= DMY pull_group2_name= DNP pull_coord1_type= umbrella pull_coord1_geometry= direction_periodic pull_coord1_groups = 1 2 pull_coord1_dim = N N Y pull_coord1_rate= 0.01 pull_coord1_k = 1000 pull_start = yes I am getting an error message and several warnings. The error reads "Invalid enum 'yes' for variable pull, using 'no' Next time use one of: 'no' 'umbrella' 'constraint 'constant force.' The warnings read "unknown left-hand 'pull_ngroups' in parameter file", with similar warnings for the other left-hand terms. I tried to compile a version using my old pull code from the earlier version just to see what would happen and it gave fewer warnings, though it didn't recognize "pull_vec1." So neither the old options nor the new options work. I would love some clarification on this issue. Thanks, Stella Nickerson -- 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] g_order
I'm simulating an ionic liquid/water liquid-liquid interface. The IL has an alkyl chain hanging off a ring, and previous simulations have found ordering of the IL at the liquid-liquid surface as the molecules essentially lay themselves flat against the interface. I though Sz might illustrate that. The interface is perpendicular to the z vector. I tried a few different commands. The latest was: g_order_mpi -f mdDone.trr -s md.tpr -n ndx-order.ndx -sl 50 -o order.xvg I can't figure out how to input the boolean for -szonly. I've tried "yes" "true" and "1" and it always tells me that's an "invalid command line argument." On Thu, Sep 10, 2015 at 1:44 PM, Justin Lemkul wrote: > > > On 9/10/15 1:58 PM, Stella Nickerson wrote: > >> I have a molecule with a carbon chain attached to a ring. I want to use >> g_order to generate the ordering parameter across the simulation box. I've >> read the manual entry for g_order, and it said to create an index file >> with >> only the "relevant" atoms included, so I made a group with just the atoms >> in the carbon chain and put it in an index file on its own with no other >> groups. >> >> The output file doesn't have any profile in it. It says the x axis is >> "Atom" which I don't want--I want the x axis to be "z" and the y axis to >> be >> "Sz." >> >> I've been playing with the arguments but nothing I try seems to make a >> difference. >> >> What am I doing wrong? >> >> > Without seeing your command(s), hard to say, but in principle you should > be able to get this with some combination of -sl -szonly, etc. Normal > usage of g_order is for alkyl chains of membranes, to calculate deuterium > order parameters. I'm not clear if that's what you actually want. > > -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] g_order
I have a molecule with a carbon chain attached to a ring. I want to use g_order to generate the ordering parameter across the simulation box. I've read the manual entry for g_order, and it said to create an index file with only the "relevant" atoms included, so I made a group with just the atoms in the carbon chain and put it in an index file on its own with no other groups. The output file doesn't have any profile in it. It says the x axis is "Atom" which I don't want--I want the x axis to be "z" and the y axis to be "Sz." I've been playing with the arguments but nothing I try seems to make a difference. What am I doing wrong? - Stella Nickerson -- 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] OPLS forcefield amide charge
Thanks! On Fri, Aug 28, 2015 at 9:57 AM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hey. > > I am extremely sorry about the incorrect reference. I should have been > careful. You should find the right charges in the supporting information of > the following paper. > http://www.ncbi.nlm.nih.gov/pubmed/22901375 > > Goodluck! > > Pallavi Banerjee. > -- > 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] OPLS forcefield amide charge
I am simulating a polymer using the OPLS forcefield. The polymer has a sidechain with a secondary amide. Using the atom charges given in the forcefield, the amide group (N, O, 2Cs, 2 Hs) has a net negative charge. I don't understand why this is so, since to my knowledge amides are not generally negatively charged. When repeated several times, the sidechain gives my polymer a net negative charge, when in real life the polymer is neutral. I'm not sure what to do. I don't want to just arbitrarily adjust the charges in the forcefield, but I don't understand why the forcefield charges work out this way unless the forcefield is flawed. Can I just slightly adjust the charges in the amide group to come out neutral. That seems... wrong. -- 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] OPLS and GROMOS forcefields
Hi, I'm simulating a polymer dissolved with an ionic liquid. Would it be possible to use the OPLS forcefield for the solvent and the GROMOS forcefield for the particle, or would that result be inherently meaningless? Thanks, Stella -- 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] Lumping different molecule types together as "rest"
I'm simulating a system with four different types of molecules. When I try to look at the energies between different types of molecules, it only lists two of the types, and lumps the other two together as "rest." As in "BMI-rest." Why is this happening? Thanks, Stella -- 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] How to exclude atoms within the same molecule from an rdf.
Thanks. On Thu, Nov 6, 2014 at 2:34 PM, João M. Damas wrote: > It's fairly "simple": generate a .tpr file with a nrexcl big enough to > exclude "self-counts" and give it to g_rdf through the -s flag. > > João > > On Thu, Nov 6, 2014 at 8:42 PM, Stella Nickerson < > stella.nicker...@gmail.com > > wrote: > > > I'm simulating a mixture of molecules (call them Molecules A, B, and C). > > The rdf between A and B and between A and C both look fine, but the one > > between A and A is crazy-looking. I assume this is because it's comparing > > atoms within the same molecule. I can't figure out how to exclude atoms > in > > the same molecule from the rdf. > > > > Thanks, > > > > Stella > > -- > > 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. > > > > > > -- > João M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 > -- > 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] How to exclude atoms within the same molecule from an rdf.
I'm simulating a mixture of molecules (call them Molecules A, B, and C). The rdf between A and B and between A and C both look fine, but the one between A and A is crazy-looking. I assume this is because it's comparing atoms within the same molecule. I can't figure out how to exclude atoms in the same molecule from the rdf. Thanks, Stella -- 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] Spacial density map
I am simulating an ionic liquid, and I want to generate a spatial density map on the anion around the cation. I want an image that looks like this: http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/Articleimage/2013/CP/c3cp53492h/c3cp53492h-f4.gif That is, I want the isosurface of the cation right around one anion. The people who made that image say they used VMD, but I can't figure out how to do it. I try to use g_spatial, but I get a density map every anion in the box (a big white cloud. Not useful). First I ran: trjconv -s md.tpr -f mdDone.trr -o noPBC.trr -pbc mol -ur compact -center with the cation as the group to be centered and the entire system as the output group. Then I ran: trjconv -s md.tpr -f noPBC.trr -o fit.trr -fit rot+trans Then I ran: g_spatial -f fit.trr -s md.tpr -nab 20 (nab 20 because -nab 10 resulted in a sigmentation fault.) I also tried making an index file defining exactly one cation as it's own index group and used that as the solute. That didn't seem to change anything. -- 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] g_spatial
I am simulating an ionic liquid, and I want to generate a spatial density map on the anion around the cation. I want an image that looks like this: http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/Articleimage/2013/CP/c3cp53492h/c3cp53492h-f4.gif That is, I want the isosurface of the cation right around one anion. The people who made that image say they used VMD, but I can't figure out how to do it. I try to use g_spatial, but I get a density map every anion in the box (a big white cloud. Not useful). First I ran: trjconv -s md.tpr -f mdDone.trr -o noPBC.trr -pbc mol -ur compact -center with the cation as the group to be centered and the entire system as the output group. Then I ran: trjconv -s md.tpr -f noPBC.trr -o fit.trr -fit rot+trans Then I ran: g_spatial -f fit.trr -s md.tpr -nab 20 (nab 20 because -nab 10 resulted in a sigmentation fault.) I also tried making an index file defining exactly one cation as it's own index group and used that as the solute. That didn't seem to change anything. -Stella -- 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] Pull code with dummy atom as reference - not working
Thanks, using direction geometry worked well. Since you seem to be very knowledgeable about this particular area, would you mind another question--When my particle passes through the less viscous to the more viscous liquid, it hovers at the interface for several picoseconds before bursting forward, shoving molecules out of its way. I've tried increasing pull_k1. If I increase it too high, it messes up pressure scaling and chaos reigns, but k1 < 3000 doesn't seem to get it through the viscous liquid. Is the pull code just not practical for this system? Because if so, I'm going to have to figure out another way to generate a PMF. Thanks again! On Wed, Jul 23, 2014 at 1:32 PM, Justin Lemkul wrote: > > > On 7/23/14, 4:04 PM, Stella Nickerson wrote: > >> I want to pull a carbon particle (170 atoms in a lattice) across an >> interface between Liquid A and Liquid B. The particle starts out in >> Liquid >> A with the center of mass at about x = 2.5 y = 2.5 z = 2.5. The >> liquid-liquid interface is at about z = 5. I want to pull the particle in >> a straight line in the positive z direction. So I put a dummy atom (no >> interaction perameters) in Liquid B at x = 2.5 y = 2.5 z = 7.5 to use as a >> reference. I put the dummy atom in a freeze group to keep it from moving. >> This is my pull code in my .mdp file, plus the freeze group code (DMY is >> the dummy atom, DNP is the carbon particle): >> >> ; Pull code >> pull= umbrella >> pull_geometry = distance ; simple distance increase >> pull_dim= N N Y >> pull_start = yes ; define initial COM distance > 0 >> pull_ngroups= 1 >> pull_group0 = DMY >> pull_group1 = DNP >> pull_rate1 = -0.01 ; 0.01 nm per ps = 10 nm per ns >> pull_k1 = 1000 ; kJ mol^-1 nm^-2 >> >> ; Define dummy atom as freeze group >> freezegrps = DMY >> freezedim = Y Y Y >> >> At first I used a negative pull rate because this tutorial ( >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> gmx-tutorials/umbrella/05a_pull_tips.html >> ) >> says to use a negative pull rate if you want to decrease the distance >> between pull_group0 and pull_group1. But instead of moving in a straight >> line in the positive z direction, the particle moved in the negative z >> direction at an angle (could this be because of periodic boundary >> conditions?) >> >> > The negative pull_rate doesn't make sense when the reference group has a > larger z-coordinate than the pulled group. Perhaps I need to clean up that > language in the tutorial. Here, a positive pull_rate or "direction" > geometry with pull_vec1 specified explicitly should do what you want. > > > When I tried to use a positive pull rate the particle just shuffled around >> in a little x-y circle. >> >> > Try direction or position geometry with an explicit pull vector. You may > also need to toy with the value of pull_k1, depending upon the viscosity of > your liquids (resisting the movement of a large particle). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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] Pull code with dummy atom as reference - not working
I want to pull a carbon particle (170 atoms in a lattice) across an interface between Liquid A and Liquid B. The particle starts out in Liquid A with the center of mass at about x = 2.5 y = 2.5 z = 2.5. The liquid-liquid interface is at about z = 5. I want to pull the particle in a straight line in the positive z direction. So I put a dummy atom (no interaction perameters) in Liquid B at x = 2.5 y = 2.5 z = 7.5 to use as a reference. I put the dummy atom in a freeze group to keep it from moving. This is my pull code in my .mdp file, plus the freeze group code (DMY is the dummy atom, DNP is the carbon particle): ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group0 = DMY pull_group1 = DNP pull_rate1 = -0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 ; Define dummy atom as freeze group freezegrps = DMY freezedim = Y Y Y At first I used a negative pull rate because this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html ) says to use a negative pull rate if you want to decrease the distance between pull_group0 and pull_group1. But instead of moving in a straight line in the positive z direction, the particle moved in the negative z direction at an angle (could this be because of periodic boundary conditions?) When I tried to use a positive pull rate the particle just shuffled around in a little x-y circle. What am I doing wrong? -- 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.
