[gmx-users] Re: compressing a system
Moeed
lecielll at googlemail.com
Sun Mar 20 23:40:20 CET 2011
On 20 March 2011 15:23, Justin A. Lemkul <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?
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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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