[gmx-users] freeze group

[subarna thakur]

I running the simulation of a protein with Fe4s4 cluster. The parameters for the cluster were obtained from a previously published paper. I have been able to carry out energy minimization with the following keywords-
--------------------------------------------------------;
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 2000
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
----------------------------------------------------------------------
The output showsSteepest Descents converged to Fmax < 2000 in 203 steps
Potential Energy = -5.8639745e+06
Maximum force = 1.7305787e+03 on atom 777
Norm of force = 4.4084099e+01
 
But when I am trying the position retraining step, with following keywords in pr.mdp file-------------------------------------------------------------
title = Yo
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 10000 ; total 20.0 ps.
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.4
; Berendsen temperature coupling is on 
Tcoupl = v-rescale
tc-grps = Protein SOL SF4 
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300 
; Energy monitoring
energygrps = Protein SOL SF4
; Pressure coupling is on
Pcoupl = parrinello-rahman
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
----------------------------------------------------------------
an error is generated with LINCS warning----Step 155, time 0.31 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms inf, max 14002532367890120704.000000 (between atoms 5093 and 5096)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1193 1195 40.1 0.1330 0.1913 0.1330
1193 1194 38.7 0.1230 0.1757 0.1230
1191 1192 77.7 0.1530 210.9258 0.1530
1189 1193 63.7 0.1530 193.1889 0.1530
1189 1190 75.9 0.1530 193.1568 0.1530
1188 1192 65.6 0.1470 893.4214 0.1470
1188 1189 67.7 0.1470 909.7200 0.1470
1186 1188 72.8 0.1330 3701.8413 0.1330
1186 1187 78.6 0.1230 3824.8157 0.1230
1184 1185 79.5 0.1780 57.6559 0.1780
1183 1184 79.3 0.1829 539.6799 0.1830
1182 1183 85.5 0.1530 3695.6021 0.1530
1181 1186 84.6 0.1530 14910.0859 0.1530
1181 1182 86.6 0.1530 15403.3672 0.1530
1179 1181 87.4 0.1470 35502.0234 0.1470
1179 1180 89.9 0.1000 1119163.2500 0.1000
1177 1179 86.7 0.1330 37732.0156 0.1330
1177 1178 85.9 0.1230 17608.4004 0.1230
1175 1177 99.6 0.1530 50041.0938 0.1530
1175 1176 102.3 0.1530 37907.5586 0.1530
1173 1175 117.7 0.1470 698413.0625 0.1470
1173 1174 120.6 0.1000 677364.4375 0.1000
1171 1173 107.2 0.1330 4168765.5000 0.1330
1171 1172 108.5 0.1230 4103918.2500 0.1230
1169 1170 112.9 0.1090 9872814.0000 0.1090
1167 1169 92.1 0.1390 68041384.0000 0.1390t = 0.310 ps: Water molecule starting at atom 196197 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
---------------------------------------------------------------------------------------------
 
These atoms 5093 and 5096 are the Iron atoms of the cluster.
 
Now My question is-
a) Can I freeze the movement of the Fe4S4 cluster during simulation by incorporating the cluster in freeze group?
b) If yes, then how do I incorporate the freeze group in Pr.mdp file during position restraining step?
c) Is there any other alternative to correct the linc warning error?


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