Thank you Vedat!!!<br><br><div class="gmail_quote">On Tue, Feb 28, 2012 at 8:35 PM, vedat durmaz <span dir="ltr"><<a href="mailto:durmaz@zib.de">durmaz@zib.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<u></u>
<div text="#000000" bgcolor="#ffffff">
<br>
hi jan/steven (?),<br>
<br>
you should know, in contrast to let's say justin lemkul, i haven't
that much experience with molecular simulations! <br>
<br>
actually, i don't expect large differences in
conformational/statistical properties depending on the usage of
lincs constraints. usually i use them when simulating target ligand
systems with explicit solvent in order to save time. for these large
systems (in the order of 100,000 atoms), i set emtol to about 300. <br>
<br>
however, for this small peptide (33AA) i refrained from constraints
and set emtol to 5 which is achieved quite quickly. for a large
protein with implicit solvent i would probably set emtol to 50 or
something like that.<br>
<br>
<br>
according to your strange results: <br>
<br>
i remember, i didn't do the energy minimization of the small peptide
on our computing cluster but on my local machine (six cpu-cores)
with gromacs-4.5.5 (no mpich, but openmpi). besides, i parameterized
my peptide using acpype (amber99sb force field) and didn't use
editconf (didn't set any box)! i just grompped the system and did
the mdrun like<br>
<br>
grompp -f ../em.mdp -c ../peptide.pdb -p ../peptide.top -o em.tpr<br>
mdrun -v -deffnm em<br>
<br>
and that's all .. 4 cores were used by mdrun.<br>
<br>
hope, that helps<br>
<br>
vedat<br>
<br>
<br>
<br>
<br>
<br>
Am 28.02.2012 17:56, schrieb Steven Neumann:
<div><div class="h5"><blockquote type="cite">
<div class="gmail_quote">
<div>I run energy minimization of my protein with implicit
solvent:</div>
<div> </div>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">
<div><span lang="EN">
<p>constraints = none</p>
<p>integrator = steep</p>
<p>dt = 0.001 ; ps</p>
<p>nsteps = 30000</p>
<p>vdwtype = cut-off</p>
<p>coulombtype = cut-off</p>
<p>pbc = no</p>
<p>nstlist = 0</p>
<p>ns_type = simple</p>
<p>rlist = 0 ; this means all-vs-all (no cut-off), </p>
<p>which gets expensive for bigger systems</p>
<p>rcoulomb = 0</p>
<p>rvdw = 0</p>
<p>comm-mode = angular</p>
<p>comm-grps = Protein</p>
<p>optimize_fft = yes</p>
<p>;</p>
<p>; Energy minimizing stuff</p>
<p>;</p>
<span lang="EN">
<p>emtol = </p>
</span><font face="Courier New" size="1"><font face="Courier New" size="1"><span lang="EN-GB">5.0</span></font></font></span><font face="Courier New" size="1"><font face="Courier New" size="1"><span lang="EN-GB"></span></font></font><span lang="EN-GB"></span><font face="Courier New" size="1"><font face="Courier New" size="1"><span lang="EN-GB"></span></font></font><span lang="EN-GB"></span><span lang="EN-GB"></span><font size="1"><span lang="EN">
<p>emstep = 0.01</p>
<p>;</p>
<p>; Implicit solvent</p>
<p>;</p>
<p>implicit_solvent = GBSA</p>
<p>gb_algorithm = OBC</p>
<p>nstgbradii = 1</p>
<p>rgbradii = 0 ; [nm] Cut-off for the calculation of
the </p>
<p>Born radii. Currently must be equal to rlist</p>
<p>gb_epsilon_solvent = 80 ; Dielectric constant for the
implicit solvent</p>
<p>; gb_saltconc = 0 ; Salt concentration for implicit
solvent </p>
<p>models, currently not used</p>
<p>sa_algorithm = Ace-approximation</p>
<p>sa_surface_tension = 2.25936</p>
</span></font></div>
</blockquote>
<div> </div>
<div>And I obtained:</div>
<div> </div>
<div><span lang="EN">
<p>Steepest Descents:</p>
<p>Tolerance (Fmax) = 1.00000e+03</p>
<p>Number of steps = 30000</p>
<p>Step Time Lambda</p>
<p>0 0.00000 0.00000</p>
<p> </p>
<p>Steepest Descents converged to Fmax < 1000 in 1 steps</p>
<p>Potential Energy = inf</p>
<p>Maximum force = 0.0000000e+00 on atom 0</p>
<p>Norm of force = nan</p>
<p> </p>
<p>Can you please explain?</p>
<p> </p>
<p>Steven</p>
</span><font size="1"><br>
</font></div>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">
<div>
<div>
<div class="gmail_quote">On Tue, Feb 28, 2012 at 2:29 PM,
Vedat Durmaz <span dir="ltr"><<a href="mailto:durmaz@zib.de" target="_blank">durmaz@zib.de</a>></span> wrote:<br>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">
<div text="#000000" bgcolor="#ffffff">actually, as far
as i know, the -DFLEXIBLE argument has no effect on
simulations without explicit water ?!<br>
<br>
i just copied the "define" line from my explicit
simulation systems .. so, the only define value,
that has a meaning is -DPOSRESHELIX.<br>
<br>
i didn't use constraints for the first time in my
life since implicit solvent simulations incorporate
a much smaller number of atoms and are therefore not
that expensive computationally. i always use this
setting for my explicit simulations only in order to
increase the step size to 2fs with a clear
conscience ...<br>
<br>
best wishes<br>
vedat<br>
<br>
<br>
Am 28.02.2012 15:18, schrieb Steven Neumann:
<div>
<div>
<blockquote type="cite">
<div>Thank you all!</div>
<div> </div>
<div>How about -DFLEXIBLE in both em and md?</div>
<div> </div>
<div>Steven<br>
<br>
</div>
<div class="gmail_quote">On Tue, Feb 28, 2012
at 2:13 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">
<div><br>
<br>
lina wrote:<br>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">On Tue, Feb 28,
2012 at 10:07 PM, Steven Neumann <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>>
wrote:<br>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">Thank you
Vedat!<br>
<br>
Why do you use -DFLEXIBLE in md and
in em?<br>
Why dont you use constraint
algorithm (LINCS) in your
simulation?<br>
</blockquote>
<br>
Otherwise, the system is easily
explode with lots of LINCS warning.<br>
<br>
</blockquote>
<br>
</div>
A system that is unstable will cause the
LINCS algorithm to fail, but turning off
constraints does not prevent a system from
becoming unstable or crashing.<br>
<br>
-Justin
<div>
<div><br>
<br>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">Also
thanks Vedat for sharing,<br>
<br>
Best regards,<br>
<br>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">Steven<br>
<br>
On Tue, Feb 28, 2012 at 12:14 PM,
Vedat Durmaz <<a href="mailto:durmaz@zib.de" target="_blank">durmaz@zib.de</a>>
wrote:<br>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote"><br>
hi steven,<br>
<br>
i've been simulating a 33 AA
peptide for the past two days
using implicent<br>
solvent in order to achieve a
proper folding.<br>
<br>
i haven't added counterions,
however, the systems shows nice
results<br>
according to what i've expected.
the mdrun command (for the
extension) for<br>
our hardware looks as follows:<br>
<br>
mpiexec -np 4 mdrun -pd -s
md.tpr -append -cpi md.cpt
-deffnm md 2>&1<br>
<br>
and here's the mdp file for the
energy minimization:<br>
<br>
define =
-DFLEXIBLE<br>
constraints = none<br>
integrator = steep<br>
dt = 0.001
; ps<br>
nsteps = 30000<br>
vdwtype = cut-off<br>
coulombtype = cut-off<br>
pbc = no<br>
nstlist = 0<br>
ns_type = simple<br>
rlist = 0 ;
this means all-vs-all (no
cut-off), which<br>
gets expensive for bigger
systems<br>
rcoulomb = 0<br>
rvdw = 0<br>
comm-mode = angular<br>
comm-grps = Protein<br>
optimize_fft = yes<br>
;<br>
; Energy minimizing stuff<br>
;<br>
emtol = 5.0<br>
emstep = 0.01<br>
;<br>
; Implicit solvent<br>
;<br>
implicit_solvent = GBSA<br>
gb_algorithm = Still ;
HCT ; OBC<br>
nstgbradii = 1<br>
rgbradii = 0 ;
[nm] Cut-off for the calculation
of the Born<br>
radii. Currently must be equal
to rlist<br>
gb_epsilon_solvent = 80 ;
Dielectric constant for the
implicit<br>
solvent<br>
; gb_saltconc = 0 ;
Salt concentration for implicit
solvent<br>
models, currently not used<br>
sa_algorithm =
Ace-approximation<br>
sa_surface_tension = -1<br>
<br>
<br>
and for the md run:<br>
<br>
define =
-DPOSRESHELIX ; -DFLEXIBLE
-DPOSRES<br>
constraints = none<br>
integrator = md<br>
dt = 0.001 ;
ps<br>
nsteps =
1000000000 ; 100000 ps = 100 ns<br>
nstcomm = 10<br>
nstcalcenergy = 10<br>
nstxout = 1000
; frequency to write coordinates
to output<br>
trajectory<br>
nstvout = 0 ;
frequency to write velocities to
output<br>
trajectory; the last velocities
are always written<br>
nstfout = 0 ;
frequency to write forces to
output<br>
trajectory<br>
nstlog = 1000
; frequency to write
energies to log<br>
file<br>
nstenergy = 1000
; frequency to write energies to
edr file<br>
<br>
vdwtype = cut-off<br>
coulombtype = cut-off<br>
<br>
pbc = no<br>
<br>
nstlist = 0<br>
ns_type = simple<br>
rlist = 0 ;
this means all-vs-all (no
cut-off), which<br>
gets expensive for bigger
systems<br>
rcoulomb = 0<br>
rvdw = 0<br>
<br>
comm-mode = angular<br>
comm-grps = system<br>
<br>
optimize_fft = yes<br>
<br>
; V-rescale temperature coupling
is on<br>
Tcoupl = v-rescale<br>
tau_t = 0.1<br>
tc_grps = system<br>
ref_t = 300<br>
; Pressure coupling is off<br>
Pcoupl = no<br>
; Generate velocites is on<br>
gen_vel = yes<br>
gen_temp = 300<br>
gen_seed = -1<br>
<br>
;<br>
; Implicit solvent<br>
;<br>
implicit_solvent = GBSA<br>
gb_algorithm = Still ;
HCT ; OBC<br>
nstgbradii = 1<br>
rgbradii = 0 ;
[nm] Cut-off for the calculation
of the Born<br>
radii. Currently must be equal
to rlist<br>
gb_epsilon_solvent = 80 ;
Dielectric constant for the
implicit<br>
solvent<br>
; gb_saltconc = 0 ;
Salt concentration for implicit
solvent<br>
models, currently not used<br>
sa_algorithm =
Ace-approximation<br>
sa_surface_tension = -1<br>
<br>
<br>
best regards,<br>
vedat<br>
<br>
<br>
Am 28.02.2012 11:59, schrieb
Steven Neumann:<br>
<br>
<blockquote style="border-left:1px solid rgb(204,204,204);margin:0px 0px 0px 0.8ex;padding-left:1ex" class="gmail_quote">Dear Gmx
Users,<br>
I am using Gromacs 4.5.4 and I
would like to implement
implicit solvent<br>
for folding of my protein. I
read mailing list and it is
still confusing for<br>
me.<br>
Is it proper to use
counterions within the system?
If not, how can I<br>
obtain netral system?<br>
Do we use cut off for vdw and
coulombic interactions?<br>
What kind of integrator should
be used with a timestep?<br>
I will appreciate an mdp file
for protein folding! Thank you<br>
Steven<br>
</blockquote>
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</div>
========================================<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>
| <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540)
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