[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
Apparently the restraints that were being used earlier were too strong. I tried weaker restraints, and that worked, with the bilayers not moving apart too quickly. Chris Neale: I did not try BD yet, but that seems to be a good idea. thank you all for the help Himanshu -- View this message in context: http://gromacs.5086.n6.nabble.com/bilayers-move-apart-by-nanometers-upon-implementing-dihedral-restraints-on-lipid-tails-tp4999188p4999258.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
Justin, Vitaly The topology is fine, I double-checked The simulation runs perfectly fine without the restraints. It is not a PBC effect, since the box size along z is 50 nm after a ns or so. Does one need yet another restraint to hold the bilayer together? There has been some discussion about problems with dihedral restrains in the list earlier, but nothing like this. -- View this message in context: http://gromacs.5086.n6.nabble.com/bilayers-move-apart-by-nanometers-upon-implementing-dihedral-restraints-on-lipid-tails-tp4999104p4999160.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
On 7/6/12 10:40 AM, khandelia wrote: Justin, Vitaly The topology is fine, I double-checked The simulation runs perfectly fine without the restraints. It is not a PBC effect, since the box size along z is 50 nm after a ns or so. Does one need yet another restraint to hold the bilayer together? I have never had a need for any restraints to keep a bilayer intact. There has been some discussion about problems with dihedral restrains in the list earlier, but nothing like this. The problem you're observing seems to indicate that your manipulation of the lipid chain causes physical instability. How extensive are the restraints? How many atoms do they involve? You provided an etc in your previous message, so I'm trying to clarify what's going on. Is it even physically possible to orient the lipid chain in such a way? You've got basically all the consecutive dihedrals in a very specific orientation - is that compatible with your system? Can you run a simulation of a single lipid in vacuo using these restraints? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
I am trying to change all lipid acyl tails to a trans orientation, and thought that restraining all tail dihedrals to 180 should work quickest. I have also tried smaller angles (120, 100) and the effect is the same, leaflets drifting apart. In fact, the 180 restraint does work fine in vacuo for a single lipid. But it is possible that the restraints are too loud. I will play with this for a little bit. The dihedrals of ALL lipid acyl tails in a typical lipid bilayer are being restrained. -- View this message in context: http://gromacs.5086.n6.nabble.com/bilayers-move-apart-by-nanometers-upon-implementing-dihedral-restraints-on-lipid-tails-tp4999104p4999164.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
I am trying to change all lipid acyl tails to a trans orientation, and thought that restraining all tail dihedrals to 180 should work quickest. I have also tried smaller angles (120, 100) and the effect is the same, leaflets drifting apart. In fact, the 180 restraint does work fine in vacuo for a single lipid. But it is possible that the restraints are too loud. I will play with this for a little bit. The dihedrals of ALL lipid acyl tails in a typical lipid bilayer are being restrained. If the force field is coarse-grained, can the problem perhaps be caused by the inconsistency between the restraint force constant and the time-step? Vitaly Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails
I am trying to implement dihedral restraints for lipids in a bilayer using what is suggested here: http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints However, although the dihedral angles seem to be restrained fine, the leaflets move apart by 10s of nanometers along +z over a nanosecond or so, after which of course, the simulation crashes. Can anyone suggest what I might be doing wrong? version 4.5.4 In the mdp file: ;dihedral restraints dihre = yes dihre_fc = 100 In the topology: [ dihedral_restraints ] 17 18 19 20 11100012 18 19 20 21 11100012 19 20 21 22 11100012 20 21 22 23 11100012 21 22 23 24 11100012 ... etc. Himanshu Himanshu - I would look for a problem in the atom numbers in your restraints. If something ususual happens (the simulation crashes), then the option works. If it works, the MDP file is most likely correct. The only other candidate is a topology file... Vitaly Dr. Vitaly V. Chaban, 430 Hutchison Hall Dept. Chemistry, University of Rochester 120 Trustee Road, Rochester, NY 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
