[gmx-users] compressing a system

[Moeed]

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.

****************************************
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:

*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
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