Thanks for your reply. So what you meant by it, that the steep option
will always be at 0K. and what this gen_temp will corresponds to?? and
SA wont have meaning for steep. Can you please help me in understanding
some things?
1. md integrator wont be a good option for minimization? since it can
take different temperature.
2. steep integrator will work on temp 0K only, whatsoever the
temperature couple or velocity generation value we provide??
These seems to be baffling.. what to use first and how to proceed?? I
have gone through manual and tutorials, but still seems confused.
Please do suggest...
regards,
Monika
David van der Spoel wrote:
Monika Sharma wrote:
Dear All,
While doing SA, I am observing that when i am using steep as option
for minimization, then the md log file generated takes ref_t as 0K
temp only, but when i am using md as integratore, the temp for ref_t
is taken as 375K( temp i gave).. See below... Its quite strange....
there is no temperature in a minimization.
+++++++++++++++++++++++++++++++++++++
log file with steep as integrator:
------------------------------------- grpopts:
nrdf: 27419.8 451854
ref_t: 0 0
tau_t: 0 0
anneal: Single Single
ann_npoints: 4 4
ann. times [0]: 0.0 2.0 4.0 6.0
ann. temps [0]: 375.0 350.0 325.0 300.0
ann. times [1]: 0.0 2.0 4.0 6.0
ann. temps [1]: 375.0 350.0 325.0 300.0
acc: 0 0 0
nfreeze: N N N
---------------------------------
-++++++++++++++++++++++++++++++++++++++++++++++
log file with md as integrator:
---------------------------------------------------------
grpopts:
nrdf: 27419.8 301239
ref_t: 375 375
tau_t: 0.1 0.1
anneal: Single Single
ann_npoints: 4 4
ann. times [0]: 0.0 2.0 4.0 6.0
ann. temps [0]: 375.0 350.0 325.0 300.0
ann. times [1]: 0.0 2.0 4.0 6.0
ann. temps [1]: 375.0 350.0 325.0 300.0
acc: 0 0 0
nfreeze: N N N
_---------------------------------------------------------------------------
The mdp file is same for both but only diff is the integrator..
Here is mdp file:
title =
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep (here the only diff as md)
nsteps = 5000
dt = 0.02
init_step = 0
;langevin dynamics
bd_fric = 0
ld_seed = 1993
;minimization
emtol = 100
emstep = 1.0
;output control
nstxout = 10
nstvout = 10
nstfout = 10
nstlog = 10
nstenergy = 10
nstxtcout = 10
xtc_precision = 100
xtc_grps =
energygrps =
; Neighbor searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.5
; electrostatics
coulombtype = PME
rcoulomb = 1.5
epsilon_r = 1.0
; van der waals params
vdwtype = cutoff
rvdw = 2.0
; table params
table-extension = 3
;PME params for ewald calc.
fourierspacing = 0.15
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; temperature coupling
tcoupl = berendsen
tc-grps = protein non-protein
tau_t = 0.1 0.1
ref_t = 375 375
; pressure coupling
pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.2
compressibility = 4.5e-5
ref_p = 1.01325
; simulated annealing params
annealing = single single
annealing_npoints = 4 4
annealing_time = 0 2 4 6 0 2 4 6
annealing_temp = 375 350 325 300 375 350 325 300
;velocity generation
gen_vel = no
gen_temp = 375
gen_seed = 1732529
-------------------------------------------------------------------------------------------------------------------
So my ques is that does that really means that SA works with md only,
not steep. Is it a bug or some reason behind it?? I have not come
across any... but with md run I am not getting any value. the run is
crashing, only the steep is showing some output, but that at 0K??
Can someone suggest anything for a succesful SA-MD?
Thanks in advance
Regards, Monika
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
