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David My starting structures are from the web site moose.bio.ucalgary.ca
<br>
i get the pdb file ,then i convert it to GRO format , do an energy minimization(withouy
problem)<br>
an then the MD ,HOW can i check that all bond and angle energies are close
to zero after the EM?<br>
<br>
THANKS<br>
<br>
<br>
<br>
<br>
David wrote:<br>
<blockquote type="cite"
cite="mid1059415414.2085.0.camel@h28n2fls34o1123.telia.com">
<pre wrap="">On Mon, 2003-07-28 at 20:53, Osmany Guirola Cruz wrote:
</pre>
<blockquote type="cite">
<pre wrap="">I have the same error in my simulation
i do a em step whitout problem but when i begin the md(whitout define =
-DPOSRES)simulations i have problem whith Lincs
i probe use shake but the method not converge ,
Please what i have to do whith my mdp files for a GREAT SIMULATION
thanks'
</pre>
</blockquote>
<pre wrap=""><!---->
such problems come from bad starting structures usually. Did you check
that all bond and angle energies are close to zero after minimizing?
</pre>
<blockquote type="cite">
<pre wrap="">nanyu101 wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear gmx-users,
I have created a bigger lipid bilayer with genconf.
genconf -f popc128a.pdb -nbox 2 2 1 -dist 0 0 0 -o popc.pdb
And this bilayer is as big as four times of former bilayer.After doing that, I have run minimization for this big bilayer with cut-off for long distance electrostatic.
title = Yo
cpp = /lib/cpp
define = -DPOSRES
constraints = none
integrator = steep
emstep = 0.001
emtol = 10
nsteps = 200000
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
pbc = xyz
ns_type = grid
coulombtype = cut-off
rlist = 1.2
rcoulomb = 1.8
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
After minimizing my big bilayer,I tried to run NPT, but the system told me this:
Using Gromacs SSE single precision assembly innerloops.
Step Time Lambda Annealing
0 0.00000 0.00000 1.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.004860 47622 47624 0.000779
After LINCS 0.000078 19562 19563 0.000009
Fatal error: Determinant = 1325213994729268314112.000000
My operation mdp file and commands are listed as follows.
cpp = /lib/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ps !
nsteps = 10000
nstcomm = 1
comm_mode = angular
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
pbc = xyz
ns_type = grid
coulombtype = cut-off
fourierspacing = 0.12
optimize_fft = yes
rlist = 1.0
rcoulomb = 1.8
rvdw = 1.4
Tcoupl = no
Pcoupl = berendsen
pcoupltype = anisotropic
tau_p = 1 1 1 0 0 0
compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
ref_p = 1 1 1 0 0 0
gen_vel = yes
gen_temp = 325.0
gen_seed = 1
editconf -f popc.pdb -o popc.gro
editconf -bt cubic -f popc.gro -o popc.gro -c -center 0 0 0 -rotate 0 0 0
grompp -f md.mdp -c popc.gro -p popc.top -o popc.tpr
mdrun -v -deffmn popc
Any comments are recommended. Thanks a lot.
best wishes,
Xianhui Wu
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<pre wrap="">
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