On 8/19/13 11:58 AM, HANNIBAL LECTER wrote:
I usually use 1.0 for my systems and I get the correct values for the
temperatures. If I couple it as a system, the low T-CNT yields a different
value than the target 300K.
What about changing the integrator to md? What happens if you remove restraints
while using sd?
-Justin
On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 8/19/13 11:42 AM, HANNIBAL LECTER wrote:
Thanks Justin.
I am not sure how it is fundamentally incompatible. Especially with
refcoord-scaling = com. Can you please provide with some more input on
that?
The refcoord-scaling option doesn't matter with frozen groups. Anything
that is frozen, by definition, never has its position updated. Under the
influence of pressure coupling, other particles around the frozen group can
have their positions scaled and thus collide with the frozen group, which
has remained in its original location.
The outputs are from g_energy.
OK, good.
Here is the .mdp file.
define = -DPOSRES_CNT
constraints = all-bonds
pbc = xyz
integrator = sd
ld_seed = 215546
dt = 0.002 ; ps !
nsteps = 50000 ; 50 ns
;nsteps = 125000 ; 250 ps
nstcomm = 10
nstcalcenergy = 10
nstxout = 0
nstxtcout = 5000 ;every 10 ps
nstvout = 100
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstlist = 10
ns_type = grid
rlist = 1.0
vdwtype = cut-off
rvdw = 1.0
coulombtype = pme
rcoulomb = 1.0
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
tc-grps = Protein CNT SOL
tau_t = 1.0 1.0 1.0
Note that tau_t is the inverse friction constant, not the "normal"
coupling constant. In this case, I don't know what appropriate values are,
especially if one of your groups is restrained. The manual advises a value
of 2.0, so at least try that. Otherwise, try coupling the System as a
whole or use a different integrator (i.e., md) to try to figure out the
origin of the problem.
-Justin
ref_t = 300.000 300 300
;freezegrps = CNT
;freezedim = Y Y Y
; Energy monitoring
energygrps = CNT Protein SOL
; energygrp-excl = CNT CNT
; Isotropic pressure coupling is now on
Pcoupl = Berendsen
refcoord-scaling = com
Pcoupltype = isotropic
tau_p = 5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300.000
gen_seed = 981487
On Mon, Aug 19, 2013 at 11:35 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 8/19/13 11:32 AM, HANNIBAL LECTER wrote:
Hi,
I have been performing NPT simulations with CNT, Protein and water.
However, when I freeze the CNT, the system crashes with segmentation
fault.
That is to be expected. Frozen atoms and pressure coupling are
fundamentally incompatible.
If I use position restraints, the temperature of the system is lower
than
what it is expected to be. I am using sd coupling.
If I couple the protein, CNT and SOL separately, the temperature of the
peptide is lower than 300K (~395K) while the temperature of the CNT is
157K. The target temperature is 300K in all cases. Can any please
explain
why such discrepancies are occurring?
Are these temperatures from g_energy or g_traj? Can you please post a
full .mdp file?
-Justin
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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