[gmx-users] Re: compressing a system
Mark Abraham
Mark.Abraham at anu.edu.au
Mon Mar 21 00:06:01 CET 2011
On 21/03/2011 9:40 AM, Moeed wrote:
>
>
> On 20 March 2011 15:23, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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.
>
>
> Thank you.
>
> 1- So You mean I should compress a chain separately and make a hexane
> box and combine these two? How is this possible to insert a solute in
> a prepared solvent box?
It is likely that you can use genconf to replicate a single hexane in a
small box (using editconf) to get something close to the right density
and size. This will have more hexane molecules in it, because some will
be removed when you use this box to solvate the PE later. Equilibrate
this box for a while.
Take your straight-chain PE and simulate it in vacuo for a bit until you
get a reasonable-looking non-extended conformation that will fit in your
intended box size. Use editconf to put your desired box around that.
Then genbox -cp non-extended-PE -cs equilibrated-hexane just like one
does for protein-in-water. This will already be about the right size
Mark
> 2- As I compress the system (NPT equilibrated to density of 0.62 g/l)
> chain takes a realistic shape, which is not extended. NVT on this
> configuration sometimes cause the chain to a more straight chain.Now I
> extracted a frame from NPT a little before equilibration (density 0.5,
> and actually this is the density I want) and equilibrated by NVT and
> no crash happened. As I asked in previous message I only want to
> assure if I can extract a frame ( even density is not equilibrated)
> followed by NVT to equilibbrate and use this as production runs.?
>
>
> -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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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