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><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div text="#000000" bgcolor="#ffffff">
<br>
</div></blockquote><div> Thank you Justin and Mark for suggestions.<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;"><div text="#000000" bgcolor="#ffffff">
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></div></blockquote><div><br> Is it not simpler if I take this PE in the right box size (editconf) and use <br><br><i><span>genbox -cp </span></i> non-extended-PE in vacuo<i><span>.gro -ci
Hexane.gro -o -nmol 110 </span></i><br><br>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:)<br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff">
<br>
Then genbox -cp -cs equilibrated-hexane just like
one does for protein-in-water. This will already be about the right
size<br></div></blockquote><div><br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div text="#000000" bgcolor="#ffffff"><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote 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><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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a 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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