<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
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:
<blockquote
cite="mid:CAKZJqQFJ9B56j398CaezyTJbvPeSJmk79KQ_z+dChx_Q5qoaVA@mail.gmail.com"
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 moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">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 class="im"><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 moz-do-not-send="true"
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 class="h5"><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
moz-do-not-send="true" 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>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the
list. Use the www<br>
interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
<br>
<br>
--<br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list.
Use the<br>
www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</blockquote>
</blockquote>
<br>
-- <br>
</div>
</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 moz-do-not-send="true" href="http://vt.edu/"
target="_blank">vt.edu</a> | <a moz-do-not-send="true"
href="tel:%28540%29%20231-9080" target="_blank"
value="+15402319080">(540) 231-9080</a><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>
========================================
<div class="HOEnZb">
<div class="h5"><br>
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div>
</div>
</blockquote>
</div>
<br>
</blockquote>
</body>
</html>