What would you suggest as a short time step? I was using 0.002 ps. And just to make sure, would 5 ns of equilibration be enough for a ~110 amino acid long protein?<br><br>Thanks,<br>Nihal<br><br><div class="gmail_quote">On Mon, Jun 20, 2011 at 7:41 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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"><div class="im">
On 20/06/2011 3:29 PM, E. Nihal Korkmaz wrote:
<blockquote type="cite">I also checked the output of the minimization:<br>
<br>
Steepest Descents converged to machine precision in 402 steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -1.81875038188621e+04<br>
Maximum force = 3.20769543152855e+02 on atom 331<br>
Norm of force = 2.04356801849931e+01<br>
<br>
I assume the structure is not relaxed enough to start a
simulation. How can I get it minimize further? I increased the
step size up to 0.1 ps, i still get the same result.<br>
</blockquote>
<br></div>
The minimization is probably OK, but a period of equilibration at a
short time step will probably help smooth the process out.
Simulations in implicit solvent have few explicit degrees of freedom
compared to explicit solvent, and might be rather more susceptible
to equilibration issues if the generated velocities are randomly
not-quite-good-enough.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">Thanks,<br>
Nihal<br>
<br>
<div class="gmail_quote">On Sun, Jun 19, 2011 at 11:48 PM, E.
Nihal Korkmaz <span dir="ltr"><<a href="mailto:enihalkorkmaz@gmail.com" target="_blank">enihalkorkmaz@gmail.com</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">Dear all,<br>
<br>
I am trying to simulate a GB simulation of a 112 amino acid
long protein. I keep getting these errors,<br>
<br>
Step 27718, time 55.436 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 33.319842, max 438.763717 (between atoms 79 and 81)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
<br>
Step 27718, time 55.436 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.058237, max 1.390675 (between atoms 91 and 93)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
91 92 50.2 0.1016 0.1065 0.1010<br>
91 93 90.0 0.1002 0.2415 0.1010<br>
91 94 70.2 0.1025 0.1066 0.1010<br>
79 80 90.0 0.1057 1.0667 0.1090<br>
79 81 90.0 1.3066 47.9342 0.1090<br>
85 86 90.0 0.1084 0.1758 0.1090<br>
85 87 90.0 1.0654 0.1668 0.1090<br>
88 89 90.0 0.1097 0.6994 0.1090<br>
88 90 90.0 0.1125 0.1097 0.1090<br>
91 92 50.2 0.1016 0.1065 0.1010<br>
91 93 90.0 0.1002 0.2415 0.1010<br>
91 94 70.2 0.1025 0.1066 0.1010<br>
<br clear="all">
<br>
I am copying my mdp parameters below, I'd appreciate any
suggestions to fix that.<br>
<br>
integrator = sd<br>
tinit = 0<br>
dt = 0.002<br>
nsteps = 2500000<br>
simulation_part = 1<br>
init_step = 1<br>
<br>
nstxout = 5000<br>
nstvout = 5000<br>
nstenergy = 500<br>
nstxtcout = 500<br>
nstlog = 500<br>
<br>
xtc_grps = System<br>
energygrps = System<br>
comm_mode = Linear<br>
; neighbor searching and vdw/pme setting up<br>
nstlist = 10<br>
ns_type = grid<br>
pbc = xyz<br>
rlist = 2.0<br>
<br>
implicit_solvent = GBSA<br>
gb_algorithm = OBC<br>
gb_saltconc = 0.15<br>
rgbradii = 2.0<br>
<br>
coulombtype = Cut-off<br>
fourierspacing = 0.1<br>
pme_order = 6<br>
rcoulomb = 2.0<br>
<br>
vdwtype = Cut-off<br>
rvdw_switch = 1.0<br>
rvdw = 2.0<br>
<br>
; cpt control<br>
tcoupl = V-rescale<br>
tc-grps = System<br>
tau_t = 0.1<br>
ref_t = 300.0<br>
<br>
Pcoupl = Berendsen<br>
pcoupltype = isotropic<br>
tau_p = 1.0<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
<br>
; velocity & temperature control<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
annealing = no<br>
constraints = hbonds<br>
constraint_algorithm = lincs<br>
morse = no<br>
<br>
<br>
Thanks,<br>
-- <br>
Elif Nihal Korkmaz<br>
<br>
Research Assistant <br>
University of Wisconsin - Biophysics <br>
Member of Qiang Cui & Thomas Record Labs<br>
1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: <a href="tel:608-265-3644" value="+16082653644" target="_blank">608-265-3644</a><br>
Email: <a href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br>
<br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Elif Nihal Korkmaz<br>
<br>
Research Assistant <br>
University of Wisconsin - Biophysics <br>
Member of Qiang Cui & Thomas Record Labs<br>
1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: <a href="tel:608-265-3644" value="+16082653644" target="_blank">608-265-3644</a><br>
Email: <a href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br>
<br>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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Research Assistant <br>University of Wisconsin - Biophysics <br>Member of Qiang Cui & Thomas Record Labs<br>1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: 608-265-3644<br>
Email: <a href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br><br><br>