Re: [gmx-users] genion with Na or Ca
Thank you for your useful replies. Turgay 2016-01-12 23:38 GMT+02:00 VITALY V. CHABAN : > Ca(2+) will block one of your binding sites, if you care. > > > > > > On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak > wrote: > > > Hi all, > > > > > > I have a quick question about neutralizing the system. I have a solvated > > system that contains a charged protein of -2q. Is there a major > difference > > betwen adding 2 Na ions and a single Ca ion to neutralize the system > > (using genion)? > > > > > > Thanks in advance, > > > > Turgay > > -- > > 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. > -- 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] genion with Na or Ca
Hi all, I have a quick question about neutralizing the system. I have a solvated system that contains a charged protein of -2q. Is there a major difference betwen adding 2 Na ions and a single Ca ion to neutralize the system (using genion)? Thanks in advance, Turgay -- 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] distribution of water molecules
Dear all, I have a box of water molecules and a peptite amphiphile based cylindirical nanofiber. I would like to find the density distribution of water. To do this: 1) I created an index file which contains OW atoms (=Oxygen atoms that belong to the water molecules) 2) Then, I used the following command: g_rdf -f traj.xtc -s OW.ndx -o rdf.gro To be able to continue one needs to choose a reference group and the other group. How does this work: for example how should I choose these groups? Also, Could the same procedures be used to compute the distribution of sodium ions? Thank you for your help. Turgay -- 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] distribution of water molecules in system
Dear Gromacs Users, I want to show distribution of water inside the peptide based cylindirical nanofiber. To do this: 1) I created an index file which contains OW atoms (=Oxygen atoms belongs to the water molecules) 2) Then, I used the following command: g_rdf -f traj.xtc -s OW.ndx -o rdf.gro In this step, I should have choosen 2-groups, that is: Select a reference group and 1 group. Question 1) I chose OW for both groups.. But, I am not sure whether this choice is correct or not.. That is, instead, should I have chosen Peptide for a reference frame and OW for group 1? Question 2) Can I also use g_rdf command to show distribution of water inside the peptide based cylindirical nanofiber? I really appreciate your help. Turgay -- 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] Covalent bond/crosslink formation with calcium
Thank you for the swift reply! We have decided against defining covalent bonds and went with the calcium-within-peptide-fiber configuration, but we have run into another problem, in that some of the calcium cations vanish from the unit cell that the fiber is in, and appear in the next unit cell, when we run an energy minimization. The missing cations are all on the same side of the peptide fiber and form a neat half-cylinder on the adjecent unit cell, so we are fairly certain that the problem has to do with our box definition. However, the entire structure is within our dodecahedral box prior to energy optimization. Is there any reason that the calciums would change position after energy minimization? Do we have to redefine our box afterwards? Thanks in advance, -Turgay 2015-02-02 15:01 GMT+02:00 Justin Lemkul : > > > On 2/2/15 7:08 AM, Turgay Cakmak wrote: > >> Dear Gromacs users, >> >> >> We are simulating a large nanofiber assembly composed of repeating units >> of >> peptides, and we have been trying to see how the addition of calcium would >> affect its behavior. We have already tried adding calcium ions in a random >> distribution, which we successfully did. >> >> >> But we also would like to insert calcium ions directly within the fiber >> structure, near areas with negative charges that the calcium cation can >> potentially bind. Is such a configuration possible (or sensible) to >> simulate in Gromacs? >> >> > Anything is possible. You'll have to justify if it's sensible :) > > >> Likewise, we would like to specify a number of covalent bonds between some >> of these side chains and the calcium ions, representing a well-crosslinked >> system. Is this possible, and if so, do you know of a suitable set of >> calcium forcefield parameters for the task? >> >> > I have never heard of such bonded parameters. People usually just modify > nonbonded parameters to get proper coordination geometry. Divalent metal > ions are quite tricky, and most force field parameters are pretty bad > approximations of the true nature of the actual interactions. > > You'll almost certainly have to derive suitable parameters, which will > involve reparametrization of charges, because charge-transfer effects would > be significant in such a complex. Simply slapping a covalent bond between > some peptide group and an ion with +2 charge is likely too crude to be > realistic. > > -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] Covalent bond/crosslink formation with calcium
Dear Gromacs users, We are simulating a large nanofiber assembly composed of repeating units of peptides, and we have been trying to see how the addition of calcium would affect its behavior. We have already tried adding calcium ions in a random distribution, which we successfully did. But we also would like to insert calcium ions directly within the fiber structure, near areas with negative charges that the calcium cation can potentially bind. Is such a configuration possible (or sensible) to simulate in Gromacs? Likewise, we would like to specify a number of covalent bonds between some of these side chains and the calcium ions, representing a well-crosslinked system. Is this possible, and if so, do you know of a suitable set of calcium forcefield parameters for the task? Best regards, and thank you in advance for your assistance. Turgay -- 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] Covalent bond/crosslink formation with calcium
Dear Gromacs users, We are simulating a large nanofiber assembly composed of repeating units of peptides, and we have been trying to see how the addition of calcium would affect its behavior. We have already tried adding calcium ions in a random distribution, which we successfully did. But we also would like to insert calcium ions directly within the fiber structure, near areas with negative charges that the calcium cation can potentially bind. Is such a configuration possible (or sensible) to simulate in Gromacs? Likewise, we would like to specify a number of covalent bonds between some of these side chains and the calcium ions, representing a well-crosslinked system. Is this possible, and if so, do you know of a suitable set of calcium forcefield parameters for the task? Best regards, and thank you in advance for your assistance -Turgay -- 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] SR and 14 terms for LJ and Coulomb interactions
Dear Gromacs Users, Thank you for your insightful comments. I am, however, still a bit confused about the non-bonded terms in potential energy, so I would be happy if you assisted me for a bit further. Is there any possible overlap between SR and 1-4 interactions? In other words, is it always true that (please assume that long-range interactions are negligible). Similarly, does hold in all possible cases? In addition, vdW and Coulombic interactions are directional. Is a vector addition necessary to get the total strength of these interactions, or does only adding up the scalar values yield an accurate sum? For the record, I am simulating a fiber composed of several hundred peptide molecules. Thank you for your time. Turgay -- 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] MD simulation at pH 2
Hi all, I have the 8-residue peptide and I want to do Molecular Dynamics simulations at pH 2 (with explicit solvent). To do this, I added three Hydrogen atoms to two of the 8-residue peptite (one Hydrogen to the Glu, two Hydrojen to the Asp). And also I choose the NH3 for the start terminus and COOH for the end terminus. Finally, I get the my peptide at pH 2. And than, I plan to follow the usual procedure (define box, fill the box with water, energy minim, md...) But, still I am not sure whether this way is correct to get simulation at pH 2 or not? Because when I look at the XXX.gro file (and also topol.top) after the pdb2gmx –f XXX.pdb, I couldn’t see the new-added hydrogens. If you could help me, I would be very happy. with my best regards, Turgay -- 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] ref_t and gen_temp
Hi all, I want to run some simulations at different temperatures (protein and solvent) changing the ref_t values. First at 300K, then 320K so on.. So, my question is: "should I also change the gen_temp value while changing the ref_t value?" Thanks and regards, Turgay -- 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.
