[gmx-users] Re: compressing a system
Justin A. Lemkul
jalemkul at vt.edu
Sun Mar 20 20:23:48 CET 2011
Moeed wrote:
> Dear experts,
>
> I am trying to build up a polymer in hexane system by increasing the
> density and use this for FE calculation. After PR step, my NVT and NPT
> trailes failed. Initially I used to get LINCS and 1-4 warnings (even for
> NVT) which were not because of flawed topology file. It turned out that
> simulations crashed just because of using -np > 4. But still even with
> this -np, NPT did not work which made me to swtich to berendsen from
> parrinelo rahman scheme. As I approched the desired density again
> simulation crashed, so I used
>
> trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300
>
> to extract one of the frames before crash then I did another NVT to
> equilibrate.
> mpirun -np 4 mdrun_mpi -deffnm PE60-110Hex-NPT-frame2300_md
>
> after around 1 ns I get the error below ( mdp file is also included). I
> described above since I encountered the situation where root cause of
> problem was not topology and just the computational issue ( I mean -np),
> I am just curious if the same thing applies here. So I have two concerns:
>
> 1- Crash at the early stages of run ( topology is working fine for a
> single hexane, so this can not be the reason). only works only for -np =<4.
>
> 2- Crash when compressing because chain crashes on itself. ( I have no
> control on this because chains takes different shapes and becomes extended)
>
>
> can you please comment on the proper settings for compressing the system.
>
> more details: There is only one polyethylene chain ( 60 units) in 110
> hexane ( box size 20 nm at the beginning) The chain is not convoluted
> and has a little extended shape that crashes on itself for long runs.
>
This is likely the problem. The compression of the system is occurring too fast
for the system to adequately respond. If the PE chain is fully extended, any
significant change in the box size (which is mostly a function of the solvent,
in this case, hexane) will case PE to interact via PBC and collapse.
> ****************************************
> Mark: Why aren't you using genbox on your polymer starting
> configuration and an equilibrated box of hexane of the right density?
>
> me: Hi, I need to work with polymer 15 Wt% system, so I manually
> calculated how many hexane I need to get this concentration. So for a
> single PE chain of 60 units I need 110 hexane. Here is the command:
>
The treatment of your system is also problematic. You need a certain
composition, but a straight PE chain with only 110 hexane will probably respond
very drastically to any non-equilibrium conditions. You need to generate a more
sensible configuration for the PE chain such that it does not collide with
itself. I would suspect that a more compact PE chain in conjunction with a
hexane box with a density closer to your target would (1) eliminate the need for
compression and (2) be more stable.
-Justin
> /genbox -cp PE60.gro -ci Hexane.gro -o PE60-110Hex.gro -nmol 110
> /
>
> /since chains is completely extended ( ~ 16 nm) I am using a cubic box
> of 20 nm and add 110 hexane which gives a very low density./
>
> //
>
> Can you please let me know how else genbox can be employed for this
> purpose>? ( if there is a better way of doing this)
>
> Also, If I compress to a density higher than needed, can I view the
> density profile and read off the time that gives the desired density and
> extract that frame ( with command above) followed by NVT to equilibrate
> and use that as prodcution run?
>
> Please help me with this.
> Thanks a lot,
> Moeed
> ===========================================
>
> step 449800, will finish Tue Mar 15 11:23:55 2011
> step 449900, will finish Tue Mar 15 11:23:55 2011
> [node5:09563] *** Process received signal ***
> [node5:09563] Signal: Segmentation fault (11)
> [node5:09563] Signal code: Address not mapped (1)
> [node5:09563] Failing at address: 0xffffffff80849dc0
> [node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10]
> [node5:09563] [ 1] mdrun_mpi [0x4f0155]
> [node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d) [0x4f9c1d]
> [node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8) [0x49c658]
> [node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19]
> [node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353]
> [node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07]
> [node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319]
> [node5:09563] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994]
> [node5:09563] [ 9] mdrun_mpi [0x420449]
> [node5:09563] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 9563 on node
> node5.reyclus.loc exited on signal 11 (Segmentation fault).
> -----------------------------------------------------------------------
>
>
>
> pbc = xyz
>
>
> ; Run control
> integrator = md
> dt = 0.002
> nsteps = 1000000 ;5000
> nstcomm = 100
>
> ; Output control
> nstenergy = 100
> nstxout = 100
> nstvout = 0
> nstfout = 0
> nstlog = 1000
> nstxtcout = 1000
>
> ; Neighbor searching
> nstlist = 10
> ns_type = grid
>
> ; Electrostatics/VdW
> coulombtype = PME
> vdw-type = Shift
> rcoulomb-switch = 0
> rvdw-switch = 0.9 ;0
>
> ; Cut-offs
> rlist = 1.25
> rcoulomb = 1.25 ;1.1
> rvdw = 1.0
>
> ; PME parameters
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
>
> ; Temperature coupling
> Tcoupl = v-rescale
> tc-grps = System ;HEX
> tau_t = 0.1 ;0.1
> ref_t = 300 ;300
>
> ; Pressure coupling
> Pcoupl = no;berendsen
> Pcoupltype = isotropic
> tau_p = 0.5 ;0.5
> compressibility = 4.5e-5 4.5e-5
> ref_p = 30 30
>
> ; Velocity generation
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
> ; Bonds
> constraints = all-bonds
> constraint-algorithm = lincs
--
========================================
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
========================================
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