Re: [gmx-users] genion command with PDB files for amber03 force field
Andrew, Just ran into this myself. If you read the notes on http://chemistry.csulb.edu/ffamber/#usage closely, you'll find this little tid-bit: If you are using ion-related GROMACS tools, such as genion, you will need to enter the AMBER ion definition to the ions.itp file in the top directory of the GROMACS distribution. This isn't too tough, as all the parameters for the ions are included with the Amber ports, but genion needs them to be in the ions.itp (or other suitable) file. Cheers, Josh On Mar 5, 2009, at 9:44 AM, drugdesign wrote: Dear gromacs users, I am using genion command to add ions to .tpr file which was made for protein by use of amber03 force field. In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI, which isnot recognized by next pdb2gmx. This is not a big problem , but it looks is a little bit like a bug. Best regards, Andrew ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Continuous polymer chain?
Hello all, Apologies if this is obvious, but I've been reading through the manual and various Google searches and come up empty-handed. My question is if it is possible to construct an infinite polymer chain in Gromacs? That is, I'd like to setup a cell with PBC, but have one end of my molecule bound to its replica across the boundary. As far as I can tell, adding extra bond records to the topology always turns my polymer into a loop in one cell. Thank you for any advice. Sincerely, Joshua Ballanco Graduate Student Department of Chemistry and Chemical Biology Stevens Institute of Technology Hoboken, NJ 07030 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Continuous polymer chain?
On Feb 6, 2009, at 1:55 PM, David van der Spoel wrote: Joshua Ballanco wrote: Hello all, Apologies if this is obvious, but I've been reading through the manual and various Google searches and come up empty-handed. My question is if it is possible to construct an infinite polymer chain in Gromacs? That is, I'd like to setup a cell with PBC, but have one end of my molecule bound to its replica across the boundary. As far as I can tell, adding extra bond records to the topology always turns my polymer into a loop in one cell. use the mdp option periodic_molecules = yes So it was something obvious I had overlooked... thanks! - Josh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Advice for simulating small DNA
On Feb 2, 2009, at 12:26 AM, Mark Abraham wrote: No, I've no idea since I don't simulate DNA. In that case, thank you the help that much more! So I'm now attempting to add restraints for the base-pair H- bonds, but I'm having trouble. It seems like no matter what I try, my system reliably explodes within the first 1 ns. My constraints look like this: [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 18 136 1 0 2 0.0 2.0 2.1 1.0 14 134 1 0 2 0.0 2.0 2.1 1.0 43 114 1 0 2 0.0 2.0 2.1 1.0 39 112 1 0 2 0.0 2.0 2.1 1.0 68 92 1 0 2 0.0 2.0 2.1 1.0 64 90 1 0 2 0.0 2.0 2.1 1.0 I've tried pre-equilibrating for up to 100 ps, but even that doesn't prevent the system from eventually exploding. Your .mdp settings for distance restraints may also be relevant here - not least in setting the existence and magnitude of these restraints. As I understand, the only relevant lines are: constraints = all-bonds integrator = md disre = simple disre-fc and others are also relevant. See manual chapter 7. Thanks for the pointer. I had overlooked most of the options there, since I'm not actually doing anything related to NMR. (That'll teach me to read more carefully!) Unfortunately, playing around with this, disre-tau, disre-weighting, and the weighting factors for each bond have not, so far, avoided the explosion. OK, that's no longer surprising - distance restraints will not usefully fix a broken model physics. Well, yes, but I also wouldn't expect them to break the broken physics further... I realize the system I was using originally was rather unphysical, but the DNA helix at least was at least *mostly* holding together. When I add the distance restraints, even with very large multipliers, the seem to serve only to tear apart the helix. Odd... For PME I was using: coulombtype = PME rlist = 0.55 rcoulomb= 0.55 rvdw= 0.55 fourierspacing = 0.1375 I agree with Justin that these are very weird for normal usage. Thanks for pointing that out. I'm relatively new with Gromacs, and hastily reduced these values to fix the relatively small box my system fits in. I doubled the short box dimension (triclinic; was -- 2.0, 2.1, 1.1 now -- 2.0, 2.1, 2.0) and increased the radii to the (as far as I can tell) more recommended values: coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 Well, that's more like it. Values for these parameters are actually intrinsic to the forcefield parametrization process, and one should vary them only with caution. This algorithmic constraint sets a minimum size for the simulation, of course. When using PBC, just fitting your system into a box doesn't address the real issue. In a real solution this 3-mer would be close to infinite dilution, which can't be modeled without a serious chunk of solvent around it. This consideration dwarfs the algorithmic one I refer to above. Unfortunately, even with all of these changes, I'm still getting an explosion (and my simulation is quite a bit slower). Anyone can get quick random numbers - you don't even need a simulation package :-P There's no substitute for background literature reading, doing tutorials, and experimenting with preparedness for failure. :-) Agreed, and thank you for all the help. I've decided to get a bit creative, and work around the whole short-DNA fragment issue all together. The new approach will also reduce the number of simulations I'm looking at doing from ~6000 to ~20, so I don't have to worry about the larger boxes taking so much longer to simulate. Again, thanks for everything! - Josh___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Advice for simulating small DNA
Hi, I'm attempting to model a system involving a small DNA 3-mer. Without any explicit constraints, the helix begins to come apart around 0.75 ns to 1 ns into the simulation. So I'm now attempting to add restraints for the base-pair H-bonds, but I'm having trouble. It seems like no matter what I try, my system reliably explodes within the first 1 ns. My constraints look like this: [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 18 136 1 0 2 0.0 2.0 2.1 1.0 14 134 1 0 2 0.0 2.0 2.1 1.0 43 114 1 0 2 0.0 2.0 2.1 1.0 39 112 1 0 2 0.0 2.0 2.1 1.0 68 92 1 0 2 0.0 2.0 2.1 1.0 64 90 1 0 2 0.0 2.0 2.1 1.0 I've tried pre-equilibrating for up to 100 ps, but even that doesn't prevent the system from eventually exploding. If, however, I remove the distance restraints, the simulation has no problem. I've also tried instead of having distance_restraints, using a harmonic potential ([ bond ] with type=6), but I haven't been able to find any suggestions for parameterizing the harmonic potentials. I played with a few values, but even the harmonic potential is causing the system to explode. I'm currently using the GROMOS96 53a6 force field with a triclinic box (~2, ~2, ~1,2), PME with grid spacing 1.375, two component v-rescale T- coupling, and no P-coupling. I'm using a 2 fs step, and I'd like to avoid having to change any parameters that will have an impact on run time (I'm less concerned about strict physical accuracy as I am with the ability to run ~6000 of these simulations in a reasonable amount of time). If anyone has any advice, I'd greatly appreciate it. Thanks! Sincerely, Joshua Ballanco Graduate Student Department of Chemistry and Chemical Biology Stevens Institute of Technology Hoboken, NJ 07030 E-mail: jball...@gmail.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Advice for simulating small DNA
On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote: Joshua Ballanco wrote: Hi, I'm attempting to model a system involving a small DNA 3-mer. Without any explicit constraints, the helix begins to come apart around 0.75 ns to 1 ns into the simulation. Presumably you have a 3-mer of helices, of which at least one comes apart. Does a single helix in water survive? (Giving a better description of your simulation system would be a good idea!) Apologies for not being more descriptive... It is a single strand of DNA containing 3 A-T base pairs. The system also contains a single Arginine residue. Simulating it in water leads to the single DNA strand gradually coming apart. With the DNA and water alone, the helix stays together much longer, but still eventually comes apart. So I'm now attempting to add restraints for the base-pair H-bonds, but I'm having trouble. It seems like no matter what I try, my system reliably explodes within the first 1 ns. My constraints look like this: [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 18 136 1 0 2 0.0 2.0 2.1 1.0 14 134 1 0 2 0.0 2.0 2.1 1.0 43 114 1 0 2 0.0 2.0 2.1 1.0 39 112 1 0 2 0.0 2.0 2.1 1.0 68 92 1 0 2 0.0 2.0 2.1 1.0 64 90 1 0 2 0.0 2.0 2.1 1.0 I've tried pre-equilibrating for up to 100 ps, but even that doesn't prevent the system from eventually exploding. Your .mdp settings for distance restraints may also be relevant here - not least in setting the existence and magnitude of these restraints. As I understand, the only relevant lines are: constraints = all-bonds integrator = md disre = simple For PME I was using: coulombtype = PME rlist = 0.55 rcoulomb= 0.55 rvdw= 0.55 fourierspacing = 0.1375 If, however, I remove the distance restraints, the simulation has no problem. Hmmm? This seems to contradict what you say above. What I meant to say is that if I remove the line disre = simple, then the simulation has no problem (other than the helix coming apart). With restraints, the system eventually explodes. Thanks for taking a look! Cheers, Josh___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Advice for simulating small DNA
On Feb 1, 2009, at 8:22 PM, Mark Abraham wrote: Joshua Ballanco wrote: On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote: Joshua Ballanco wrote: Hi, I'm attempting to model a system involving a small DNA 3-mer. Without any explicit constraints, the helix begins to come apart around 0.75 ns to 1 ns into the simulation. Presumably you have a 3-mer of helices, of which at least one comes apart. Does a single helix in water survive? (Giving a better description of your simulation system would be a good idea!) Apologies for not being more descriptive... It is a single strand of DNA containing 3 A-T base pairs. The system also contains a single Arginine residue. Simulating it in water leads to the single DNA strand gradually coming apart. With the DNA and water alone, the helix stays together much longer, but still eventually comes apart. OK, so your model physics for DNA is intrinsically broken. Where did you get it? The coordinates are from 3DNA. I'm using the terms from the G53a6 force field for DADE and DTHY. As for the H-bond physics, I've thus far been unable to find a good suggestion for how to handle these explicitly using Gromacs. Do you have a recommendation as to where I should be looking? (None of the primary literature I've looked through thus far seems concerned with MD of such short DNA fragments). So I'm now attempting to add restraints for the base-pair H- bonds, but I'm having trouble. It seems like no matter what I try, my system reliably explodes within the first 1 ns. My constraints look like this: [ distance_restraints ] ; ai aj type index type’ low up1 up2 fac 18 136 1 0 2 0.0 2.0 2.1 1.0 14 134 1 0 2 0.0 2.0 2.1 1.0 43 114 1 0 2 0.0 2.0 2.1 1.0 39 112 1 0 2 0.0 2.0 2.1 1.0 68 92 1 0 2 0.0 2.0 2.1 1.0 64 90 1 0 2 0.0 2.0 2.1 1.0 I've tried pre-equilibrating for up to 100 ps, but even that doesn't prevent the system from eventually exploding. Your .mdp settings for distance restraints may also be relevant here - not least in setting the existence and magnitude of these restraints. As I understand, the only relevant lines are: constraints = all-bonds integrator = md disre = simple disre-fc and others are also relevant. See manual chapter 7. Thanks for the pointer. I had overlooked most of the options there, since I'm not actually doing anything related to NMR. (That'll teach me to read more carefully!) Unfortunately, playing around with this, disre-tau, disre-weighting, and the weighting factors for each bond have not, so far, avoided the explosion. For PME I was using: coulombtype = PME rlist = 0.55 rcoulomb= 0.55 rvdw= 0.55 fourierspacing = 0.1375 I agree with Justin that these are very weird for normal usage. Thanks for pointing that out. I'm relatively new with Gromacs, and hastily reduced these values to fix the relatively small box my system fits in. I doubled the short box dimension (triclinic; was -- 2.0, 2.1, 1.1 now -- 2.0, 2.1, 2.0) and increased the radii to the (as far as I can tell) more recommended values: coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 fourierspacing = 0.12 Unfortunately, even with all of these changes, I'm still getting an explosion (and my simulation is quite a bit slower). Thanks again for the pointers. I'm going to try running everything with ffamber to see if it does a better job with the DNA (without the added restraints). I presume the port validated with Gromacs 3.3.1 is still good for 4.0? Thanks! - Josh___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
