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On 21/03/2011 9:40 AM, Moeed wrote:
<blockquote
cite="mid:AANLkTikhkq1P7o1gvw=+_JxGzHc5TW8=_EubzuEH9O0K@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On 20 March 2011 15:23, Justin A. Lemkul
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im"><br>
<br>
Moeed wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Dear experts,<br>
<br>
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<br>
<br>
trjconv -s .tpr -f .trr -o frame2300.gro -dump 2300<br>
<br>
to extract one of the frames before crash then I did
another NVT to equilibrate.<br>
mpirun -np 4 mdrun_mpi -deffnm
PE60-110Hex-NPT-frame2300_md<br>
<br>
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:<br>
<br>
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.<br>
<br>
2- Crash when compressing because chain crashes on itself.
( I have no control on this because chains takes different
shapes and becomes extended)<br>
<br>
<br>
can you please comment on the proper settings for
compressing the system.<br>
<br>
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.<br>
<br>
</blockquote>
<br>
</div>
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.
<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
****************************************<br>
Mark: Why aren't you using genbox on your polymer
starting configuration and an equilibrated box of hexane
of the right density?<br>
<br>
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:<br>
<br>
</blockquote>
<br>
</div>
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.<br>
</blockquote>
<div><br>
Thank you.<br>
<br>
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? <br>
</div>
</div>
</blockquote>
<br>
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.<br>
<br>
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.<br>
<br>
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<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTikhkq1P7o1gvw=+_JxGzHc5TW8=_EubzuEH9O0K@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div>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.?<br>
<br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
/genbox -cp PE60.gro -ci Hexane.gro -o PE60-110Hex.gro -nmol
110 /
<div>
<div class="h5"><br>
<br>
/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./<br>
<br>
//<br>
<br>
Can you please let me know how else genbox can be
employed for this purpose>? ( if there is a better
way of doing this)<br>
<br>
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?<br>
<br>
Please help me with this.<br>
Thanks a lot,<br>
Moeed<br>
===========================================<br>
<br>
step 449800, will finish Tue Mar 15 11:23:55 2011<br>
step 449900, will finish Tue Mar 15 11:23:55 2011<br>
[node5:09563] *** Process received signal ***<br>
[node5:09563] Signal: Segmentation fault (11)<br>
[node5:09563] Signal code: Address not mapped (1)<br>
[node5:09563] Failing at address: 0xffffffff80849dc0<br>
[node5:09563] [ 0] /lib64/libpthread.so.0 [0x3a2660eb10]<br>
[node5:09563] [ 1] mdrun_mpi [0x4f0155]<br>
[node5:09563] [ 2] mdrun_mpi(gmx_pme_do+0x216d)
[0x4f9c1d]<br>
[node5:09563] [ 3] mdrun_mpi(do_force_lowlevel+0x21c8)
[0x49c658]<br>
[node5:09563] [ 4] mdrun_mpi(do_force+0xc59) [0x50db19]<br>
[node5:09563] [ 5] mdrun_mpi(do_md+0x5623) [0x43e353]<br>
[node5:09563] [ 6] mdrun_mpi(mdrunner+0xa07) [0x435e07]<br>
[node5:09563] [ 7] mdrun_mpi(main+0x1269) [0x443319]<br>
[node5:09563] [ 8]
/lib64/libc.so.6(__libc_start_main+0xf4) [0x3a25e1d994]<br>
[node5:09563] [ 9] mdrun_mpi [0x420449]<br>
[node5:09563] *** End of error message ***<br>
--------------------------------------------------------------------------<br>
mpirun noticed that process rank 0 with PID 9563 on node
node5.reyclus.loc exited on signal 11 (Segmentation
fault).<br>
-----------------------------------------------------------------------<br>
<br>
<br>
<br>
pbc = xyz <br>
; Run control integrator
= md dt =
0.002 nsteps = 1000000
;5000 nstcomm = 100 <br>
; Output control<br>
nstenergy = 100 nstxout
= 100 nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000 nstxtcout
= 1000 <br>
; Neighbor searching<br>
nstlist = 10 ns_type
= grid <br>
; Electrostatics/VdW<br>
coulombtype = PME vdw-type
= Shift rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
<br>
; Cut-offs<br>
rlist = 1.25 rcoulomb
= 1.25 ;1.1 rvdw = 1.0
<br>
; PME parameters<br>
fourierspacing = 0.12 fourier_nx
= 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
pme_order = 4 ewald_rtol
= 1e-5<br>
optimize_fft = yes<br>
<br>
; Temperature coupling Tcoupl =
v-rescale tc-grps = System
;HEX tau_t = 0.1
;0.1 ref_t = 300 ;300
; Pressure coupling<br>
Pcoupl = no;berendsen
Pcoupltype = isotropic tau_p
= 0.5 ;0.5 compressibility
= 4.5e-5 4.5e-5 ref_p = 30
30 <br>
; Velocity generation gen_vel
= yes gen_temp =
300.0 gen_seed = 173529
<br>
; Bonds<br>
constraints = all-bonds
constraint-algorithm = lincs<br>
</div>
</div>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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