Frankie Montenegro wrote:
Hi again guys,
Few more questions:
1. I would like to calculate compressibility of the protein+water
system, but separating it into bulk water, hydration water and
protein. So I need to pick these and compute volumes separately. When
picking hydration water molecules, two tools are mentioned on the
List: trjorder and g_hbond. Which one would you recommend for my task?
That sounds difficult because computing volume is difficult. We should
write a better program for this, but the problem lies in definition:
where does one water molecule stop and the next begin?
2. a)The program g_energy gives output for compressibility. What
method was used for that calculation?
b) When running g_energy I noticed a particularly crappy number for
the specific heat of SPC water with ffgmx forcefield. It is about
17J/mol.K (should be about 75).
This is because of Berendsen coupling. It should be better with
Nose-Hoover or without (using shifted vdw potential as well).
I get similar number with my code using energy fluctuation method.
Do you guys have any suggestions? I cut and paste my equilibration and
production run mdp files.
----------------------------
Equilibration
----------------------------
Thanks,
Frankie
cpp = /lib/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
tinit = 0.0
dt = 0.001 ; ps !
nsteps = 10000 ; total 10 ps.
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
comm-mode = Angular
nstcomm = 1
comm-grps = System
pbc = xyz
coulombtype = PME
rvdw = 0.9
rlist = 0.9
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = System
tau_t = 0.1
ref_t = 275
; Energy monitoring
energygrps = System
; Pressure coupling is not on
Pcoupl = no
; Random seed for Andersen thermostat
andersen_seed = 815131
; Generate velocites is on at 275 K.
gen_vel = yes
gen_temp = 275.0
gen_seed = 173529
------------
NVT run
------------
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 1100000 ; total 1.1ns.
nstcomm = 1
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstlist = 10
ns_type = grid
comm-mode = Angular
nstcomm = 1
comm-grps = System
pbc = xyz
coulombtype = PME
rvdw = 0.9
rlist = 0.9
rcoulomb = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = System
tau_t = 0.1
ref_t = 275
; Energy monitoring
energygrps = System
; Pressure coupling is not on
Pcoupl = no
; Generate velocites is on at 275 K.
gen_vel = yes
gen_temp = 275.0
gen_seed = 173529
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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