[gmx-users] CG-MD simulation of protein, always crash with protein
Trang
ttdtrang at gmail.com
Thu Apr 15 18:06:57 CEST 2010
My target system is a protein with lipid molecules added randomly (using
GENBOX). Running MD, I expect to have the protein "inserted" through
self-assembly. However, I encountered the crash every different trials. So I
broke down the problem, that is, to run md simulation for the protein
molecule only, and in vacuum. Still no improvement. Although all the
distances in the minimized structure are visually proper, the system
exploded.
When I set RING_BONDS="bonds", the system crashed at the very first step.
With RING_BONDS="constraints", it exploded at about 5800 ps. It is strange
that RMSD differences at that time has been relatively constant. with such
RMSD, I think the system must be stable enough?!?!
I built the topology using the script seq2itp provided at Martini's site.
Already did some random check to see if the script works fine, special
notice was made at amino acids with ring. Should I make a more thorough
check on the itp file?
Trang
On Thu, Apr 15, 2010 at 6:32 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> It is mot likely that your preparation of the system is somehow corrupted.
> The insertion of a protein in a lipid bilayer might easily introduce strong
> forces in the system and thereby result in a crash of your simulation.
>
> It is also possible that your protein topology is not describing your
> system
> correctly. This no one can tell without knowing how you built your topology
> and for which kind of system.
>
> Note that cycle in the Martini FF (Tyr/Trp/His) use constrains and are
> therefore extremely sensible to strong forces in there environment.
>
> I would suggest you get back to the point where you insert your protein
> in the bilayer and check very carefully potential bad contact between the
> protein and the lipid. The minimization should go smooth and running
> should not be problematic.
>
> XAvier.
>
> On Apr 15, 2010, at 12:49 PM, Trang wrote:
>
> Dear gmx users,
> I'm trying to run some CG-MD with gromacs, using the available Martini FF.
> The first run with {lipid + water} is fine. The POPC lipid bilayer is
> successfully self-assembled. I then applied Martini FF for system involving
> protein.
> All the systems I've tried so far could not survive an md run for long
> enough. Most of them crashed at the very first step.
>
> I've encountered different types of errors (range checking error,
> segmentation fault...) and even hanging of the system, all of which converge
> at the same suggestion that the system hasn't been minimized/equilibrated
> well enough.
>
> I've tried some tracing back but still cannot figure out where the problem
> can be.
>
> * From screen output, I traced back to the atoms on which large force
> affect: most of the cases, these atoms belong to the ring of amino acid such
> as TRP, TYR. The worst case was that, 2 beads of 1 TRP totally overlap after
> minimization!!! The newest trial is related to atom 195 - 196 - 197, which
> are beads of the same TYR residue<http://picasaweb.google.com/lh/photo/RMSyRH801u44-EiSQjK0-A?feat=directlink>. What kind of problem can cause such a bad minimization?
>
> * From log file after crashed runs, I found the initial temperature is
> extremely high (e.g 6.67074e+12 K, etc). A colleague of mine suggest that it
> may be due to the high pressure, which in turn caused by unevenly
> distributed molecules in the input structure. This seemed to be reasonable,
> for after minimization (picture<http://picasaweb.google.com/lh/photo/bSLh3oSC5VLxwRrmpeMecQ?feat=directlink>), the distribution of water is even worse than the initial state (
> picture<http://picasaweb.google.com/lh/photo/qNEp0_FZdxiO05PqTVBsTw?feat=directlink>).
> But, I get stuck and have no idea why minimization can make system so bad.
> This is the mdp for the minimization step
>
> -------------------------------MINI-----------------------------------------------
> title = Martini
> cpp = /usr/bin/cpp
> integrator = steep
> tinit = 0.0
> dt = 0.025
> nsteps = 500
> nstcomm = 1
> comm-grps =
> nstxout = 5000
> nstvout = 5000
> nstfout = 0
> nstlog = 1000
> nstenergy = 1000
> nstxtcout = 1000
> xtc_precision = 100
> xtc-grps =
> energygrps =
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 1.2
> coulombtype = Shift
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> epsilon_r = 15
> vdw_type = Shift
> rvdw_switch = 0.9
> rvdw = 1.2
> DispCorr = No
> tcoupl = no
> Pcoupl = no
> gen_vel = no
> gen_temp = 320
> gen_seed = 473529
> constraints = none
> constraint_algorithm = Lincs
> unconstrained_start = no
> lincs_order = 4
> lincs_warnangle = 30
>
> ------------------------------------------------------------------------------------
>
>
> and this is for the next step md
>
> ------------------------------------MD--------------------------------------
> title = Martini
> cpp = /usr/bin/cpp
> integrator = md
> tinit = 0.0
> dt = 0.025
> nsteps = 50000
> nstcomm = 1
> comm-grps =
> nstxout = 5000
> nstvout = 5000
> nstfout = 0
> nstlog = 2000
> nstenergy = 2000
> nstxtcout = 1000
> xtc_precision = 100
> xtc-grps =
> energygrps =
> nstlist = 10
> ns_type = grid
> pbc = xyz
> rlist = 1.2
> coulombtype = Shift
> rcoulomb_switch = 0.0
> rcoulomb = 1.2
> epsilon_r = 15
> vdw_type = Shift
> rvdw_switch = 0.9
> rvdw = 1.2
> DispCorr = No
> tcoupl = Berendsen
> tc-grps = Protein W
> tau_t = 0.3 0.3
> ref_t = 323 323
> Pcoupl = berendsen
> Pcoupltype = isotropic
> tau_p = 3.0
> compressibility = 3e-5
> ref_p = 1.0
> gen_vel = no
> gen_temp = 323
> gen_seed = 666
> constraints = none
> constraint_algorithm = Lincs
> unconstrained_start = no
> lincs_order = 4
> lincs_warnangle = 30
>
> ------------------------------------------------------------------------------------
>
> I've struggled with this for about 2 weeks and still have no idea of where
> to fix the problem. Am I missing something too basic for tutorials to
> mention? I'm sorry for being such a newbie. I've tried my best to figure out
> the problem before asking for help. Can you give me some suggestions to get
> out of this?
> --
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100415/110d631f/attachment.html>
More information about the gromacs.org_gmx-users
mailing list