Justin, you understood it correctly; I only have problems with the low cholesterol concentration. According to g_traj -com the COM of DPPC in one of the simulations moves 0.6 nm in 3.5 ns. And as Xavier just wrote it's quite much... My mdp file looks like this:
title = dppc128 cpp = /lib/cpp include = define = integrator = md dt = 0.002 nsteps = 3500000 ; 7 ns nstlog = 25000 nstenergy = 25 nstxout = 750000 nstxtcout = 400 nstvout = 750000 nstfout = 0 xtc_grps = DPPC SOL CHOL MOL energygrps = DPPC SOL CHOL MOL nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 tcoupl = Nose-hoover tc-grps = DPPC SOL CHOL MOL tau_t = 0.1 0.1 0.1 0.1 ref_t = 323 323 323 323 Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 ref_p = 1.0 1.0 gen_vel = yes gen_temp = 323 gen_seed = 173529 constraints = all-bonds pbc = xyz optimize_fft = yes unconstrained_start = no pull = constraint pull_geometry = cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1 = 0 0 1 pull_init1 = 3.498 comm_mode = linear nstcomm = 1 comm_grps = DPPC_CHOL_MOL SOL Emma Eriksson PhD student in biophysical chemistry School of chemistry National University of Ireland - Galway Galway, Ireland ________________________________________ Från: [email protected] [[email protected]] för Justin A. Lemkul [[email protected]] Skickat: den 29 april 2010 15:44 Till: Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box ERIKSSON, EMMA wrote: > The increase in z box length is due to that I have replaced 12 DPPC lipids by > cholesterol molecules. Cholesterol reduces the area per lipid and compresses > the bilayer lateral (xy) area, resulting in a slight increase in the water > layer thickness. I have performed exactly the same simulations with a higher > concentration of cholesterol (in which the bilayer is even more compressed > and the water phase therefore is even thicker) and there is no translation in > any of the simulations. > So if I understand correctly, you have different levels of cholesterol in DPPC, and at low cholesterol concentration you get a z-translation of your membrane, but at high concentration of cholesterol, you get no translation at all? Can you plot (using g_traj -com) the motion of the membrane to quantify just how much the membrane is moving? And again I would ask that you post your entire .mdp file, just to see your settings. -Justin > > Emma Eriksson PhD student in biophysical chemistry School of chemistry > National University of Ireland - Galway Galway, Ireland > ________________________________________ Från: [email protected] > [[email protected]] för Justin A. Lemkul [[email protected]] > Skickat: den 29 april 2010 15:28 Till: Gromacs Users' List Ämne: Re: > [gmx-users] Constrained simulations crash when bilayer moves in the z > direction in the box > > ERIKSSON, EMMA wrote: >> The last section of my mdp file: >> >> pull = constraint pull_geometry = cylinder >> pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = >> DPPC pull_group1 = MOL pull_vec1 = 0 0 1 >> pull_init1 = 3.083 >> >> comm_mode = linear nstcomm = 1 comm_grps = >> DPPC_CHOL_MOL SOL >> >> With my small molecule being MOL. I'm constraining the distance between the >> DPPC and the small molecule at different distances along the z direction >> of the bilayer. This example is for the distance being 3.083 nm between the >> two groups. The total z box length is ~7.2 nm. Even when I'm running >> without constraint the system is translating in the z direction but no >> crash occurs when the pbc is crossed. >> > > At this point, it would probably be useful to understand how you set up and > build the system. The original 128-lipid DPPC from Tieleman is ~6.5 nm in > the z-dimension, so somewhere along the way you've picked up 0.7 nm. Is > there void space in your box? Did you remove the water and re-solvate? > > There is no reason (in my mind) why the bilayer should be translating in the > z-dimension at all. I've done a number of simulations with this particular > DPPC bilayer and never had a problem. Maybe you can also post your whole > .mdp file to see if there are any problems. > > -Justin > >> Emma Eriksson PhD student in biophysical chemistry School of chemistry >> National University of Ireland - Galway Galway, Ireland >> ________________________________________ Från: >> [email protected] [[email protected]] för >> Justin A. Lemkul [[email protected]] Skickat: den 29 april 2010 14:33 Till: >> Gromacs Users' List Ämne: Re: [gmx-users] Constrained simulations crash >> when bilayer moves in the z direction in the box >> >> ERIKSSON, EMMA wrote: >>> My system consists of 128 lipids and 3655 water molecules and is one of >>> the structures one can download from University of Calgary. I think that >>> the water phase is thick enough because when I run non-constrained >>> simulations and the system translates there is no crash when the lipids >>> cross the pbc. >>> >> What type of pulling are you trying to do? Can you post your .mdp file, or >> at least your pull parameters? My sense is that your pull distance is >> greater than half the box dimension in the pull direction, causing lipids >> to be pulled across PBC and break down. >> >> -Justin >> >>> Emma >>> >>> >>> ________________________________________ Från: >>> [email protected] [[email protected]] för >>> Justin A. Lemkul [[email protected]] Skickat: den 29 april 2010 14:09 Till: >>> Discussion list for GROMACS users Ämne: Re: [gmx-users] Constrained >>> simulations crash when bilayer moves in the z direction in the box >>> >>> Do you have sufficient water on either "side" of your membrane? That is, >>> are the lipids crossing PBC because of spurious interactions with the >>> other side of the membrane? That would certainly be a reason for a crash >>> - the model physics is breaking down. How did you generate your initial >>> membrane configuration? >>> >>> -Justin >>> >>> ERIKSSON, EMMA wrote: >>>> Hi again, I thought your suggestions would work for my membrane, but it >>>> seems like the removal of COM translation of the bilayer and water >>>> separately does not stop the system from translating in the box. My new >>>> simulations are now soon crashing again since the lipids are crossing >>>> the pbc. I was using two comm-grps, one containing DPPC_CHOL_MOL and >>>> one with water. How is it possible that the system still is able to >>>> translate? Is there any other way to do this? Otherwise I have to >>>> manually translate the system back to its original position in the box >>>> after the simulation has crashed and then continue the simulation, but >>>> this is not very good since I cannot use the checkpoint file then and >>>> the continuation is not exact. Any suggestion what to do? Thanks in >>>> advance. >>>> >>>> Emma >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> *Från:* [email protected] [[email protected]] >>>> för XAvier Periole [[email protected]] *Skickat:* den 27 april 2010 >>>> 16:32 *Till:* Discussion list for GROMACS users *Ämne:* Re: [gmx-users] >>>> Constrained simulations crash when bilayer moves in the z direction in >>>> the box >>>> >>>> >>>> you should remove the water and lipid bilayer COM separately. I am not >>>> sure what you should do with your small molecule though. Probably best >>>> to add it to the bilayer as you constrain their relative position! >>>> >>>> On Apr 27, 2010, at 4:32 PM, ERIKSSON, EMMA wrote: >>>> >>>>> Hi again, Thanks Xavier for your reply. I didn't know that this mdp >>>>> option existed. However, I read the manual and also checked the >>>>> mdout.mdp files for my previous simulations, and I understood it as >>>>> if those are the default settings even if you don't specify any of >>>>> them in the md.mdp file. The default comm_groups is the whole system >>>>> so I guess if I'm not writing anything there it will take the whole >>>>> system. In that case I think that in my previous simulations the >>>>> translational motion should have been removed for the whole system, >>>>> but since it's obviously not remove something is wrong. Or did I >>>>> misunderstand everything? My system consists of DPPC lipids, >>>>> cholesterol, water and one small molecule. Should I specify >>>>> comm_groups as only the lipids? In that case I get a warning from >>>>> grompp. You wrote comm-grps = membrane solvent + ions. Only the water >>>>> then? Sorry that I didn't understand you explanation. >>>>> >>>>> Emma >>>>> >>>>> >>>>> ------------------------------------------------------------------------ >>>>> *Från:* [email protected] >>>>> <mailto:[email protected]> [[email protected] >>>>> <mailto:[email protected]>] för XAvier Periole >>>>> [[email protected] <mailto:[email protected]>] *Skickat:* den 27 april >>>>> 2010 12:41 *Till:* Discussion list for GROMACS users *Ämne:* Re: >>>>> [gmx-users] Constrained simulations crash when bilayer moves in the z >>>>> direction in the box >>>>> >>>>> >>>>> The crash seems to be expected as by crossing the pbc the distance >>>>> will change significantly and in way the algorithm can not handle. >>>>> >>>>> Note that the overall translational motion of your system should >>>>> always be removed. >>>>> >>>>> The removal of the COM motion of your bilayer should be sufficient to >>>>> prevent the overall motion of the bilayer. have a look at the >>>>> following option in the mdp: ; mode for center of mass motion removal >>>>> comm-mode = Linear ; number of steps for center of mass motion >>>>> removal nstcomm = 1 ; group(s) for center of mass motion removal >>>>> comm-grps = membrane solvent+ions >>>>> >>>>> >>>>> On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote: >>>>> >>>>>> Hi all! >>>>>> >>>>>> I have a problem regarding lipid bilayer simulations in Gromacs 4. >>>>>> During some of my simulations the whole system is moving in the z >>>>>> direction in the box, meaning that after some time the lipids are >>>>>> going out in the bottom of the box and coming in in the top of the >>>>>> box, since I'm using periodic boundary conditions. This doesn't >>>>>> matter (I think) when running non-constrained simulations, however >>>>>> when I'm constraining the distance between the lipids >>>>>> (pull_geometry=cylinder) and a molecule in the system the system >>>>>> explodes and the simulations crash when the lipids are starting to >>>>>> cross over to the other side. The fact that the system is moving in >>>>>> the box must be the problem since the system explodes exactly when >>>>>> the first lipid passes over to the other side and nothing like >>>>>> this ever happens when the bilayer is not moving in the box. Is >>>>>> there any way to freeze the cylindrical COM of the lipids or >>>>>> something like that so that they stay more or less in the middle of >>>>>> the box all the time? I don't want to use freezegrps and freezedim >>>>>> = N N Y as this freezes the lipids completely in the z direction, >>>>>> and that's not what I want, I want them to be free to move as >>>>>> before but I want to stop the whole system from moving too much in >>>>>> the z direction. Anyone that has experienced a similar problem or >>>>>> know how to go about with this? I would really appreciate any help >>>>>> I can get. Thanks. >>>>>> >>>>>> Emma -- gmx-users mailing list [email protected] >>>>>> <mailto:[email protected]> >>>>>> http://lists.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 [email protected] >>>>>> <mailto:[email protected]>. Can't post? Read >>>>>> http://www.gromacs.org/mailing_lists/users.php >>>>> -- gmx-users mailing list [email protected] >>>>> <mailto:[email protected]> >>>>> http://lists.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 [email protected] >>>>> <mailto:[email protected]>. Can't post? Read >>>>> http://www.gromacs.org/mailing_lists/users.php >>> -- ======================================== >>> >>> Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT >>> Trainee 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 list >>> [email protected] http://lists.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 [email protected]. Can't post? >>> Read http://www.gromacs.org/mailing_lists/users.php >>> >> -- ======================================== >> >> Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee >> 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 list >> [email protected] http://lists.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 [email protected]. Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> > > -- ======================================== > > Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee > 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 list > [email protected] http://lists.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 [email protected]. Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list [email protected] http://lists.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list [email protected] http://lists.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
