I also noticed this error on my setup, so I changed tau-t to 0.1, which is
commonly found on others setup.
tau-t = 0.0109 seems too low.
2010/11/26 Per Larsson per.lars...@sbc.su.se
Hi!
Have never tried remd with implicit solvent, but note that the unit of
tau-t in the mdp-file is ps, not ps-1. This means you should set tau-t =
0.0109 rather than 91.
Try this and see if the problem goes away!
/Per
26 nov 2010 kl. 15:55 skrev César Ávila clav...@gmail.com:
Dear all,
I am trying to set up a REMD simulation for a peptide (CHARMM ff) in
implicit solvent (OBC GB).
Following Bjelkmar et al* I am using stochastics dynamics integration
with an inverse friction constant of 91 ps-1, 5 fs timestep,
virtual-sites for hydrogens, all-vs-all nonbonded (no cutoff). The full
.mdp file is attached at the end of this mail. The problem I am
facing is that after a while, the temperatures of all replicas start
dropping even below the lowest target temperature.
Would you suggest changing some parameter or the whole thermostat to
prevent this from happening?
@ s0 legend Temperature
0.00 310.811523
5.00 435.627045
10.00 417.161713
15.00 414.248901
20.00 399.390686
25.00 375.087219
30.00 338.131256
35.00 339.961151
40.00 319.424561
45.00 290.442322
50.00 289.587921
55.00 248.746246
60.00 253.192047
65.00 242.619476
70.00 256.051941
75.00 237.648468
80.00 231.938690
85.00 217.029953
90.00 211.447983
95.00 210.393890
100.00 208.518417
105.00 196.718445
110.00 219.245682
115.00 202.957993
120.00 193.128159
125.00 198.278198
130.00 175.304108
135.00 164.925613
140.00 195.024490
145.00 201.153046
150.00 211.160797
155.00 189.525085
160.00 191.156006
165.00 186.545242
170.00 186.885422
175.00 182.838486
180.00 174.960098
185.00 175.244049
190.00 179.517975
195.00 165.785416
200.00 189.871048
205.00 179.510178
210.00 152.527710
215.00 160.109955
220.00 163.564148
* Implementation of the CHARMM ff in GROMACS (2010) JCTC, 6, 459-466
; Run parameters
integrator = sd
dt = 0.005; ps !
nsteps = 2
nstcomm = 1
comm_mode = angular ; non-periodic system
; Bond parameters
constraints = all-bonds
constraint_algorithm= lincs
lincs-iter = 1
lincs-order = 6
; required cutoffs for implicit
nstlist = 0
ns_type = grid
rlist = 0
rcoulomb= 0
rvdw= 0
epsilon_rf = 0
rgbradii= 0
; cutoffs required for qq and vdw
coulombtype = cut-off
vdwtype = cut-off
; temperature coupling
tcoupl = v-rescale
tc-grps = system
tau-t = 91
ref-t = 300
; Pressure coupling is off
Pcoupl = no
; Periodic boundary conditions are off for implicit
pbc = no
; Settings for implicit solvent
implicit_solvent= GBSA
gb_algorithm= OBC
gb_epsilon_solvent = 78.3
sa_surface_tension = 2.25936
;Output control
nstxout = 1000
nstfout = 0
nstvout = 0
nstxtcout = 0
nstlog = 1000
nstcalcenergy = -1
nstenergy = 1000
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
gen_seed = 1993
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