[gmx-users] Re: compressing a system
Moeed
lecielll at googlemail.com
Mon Mar 21 01:29:37 CET 2011
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.
>
> Thank you Justin and Mark for suggestions.
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.
>
Is it not simpler if I take this PE in the right box size (editconf) and
use
*genbox -cp * non-extended-PE in vacuo*.gro -ci Hexane.gro -o
-nmol 110 *
so that I have exact number of solvet. (so no need to worry about removal of
some hexane after insertion PE when using command below:)
>
> Then genbox -cp -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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
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>
>
>
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