-
Notifications
You must be signed in to change notification settings - Fork 1
/
run-GaMD.sh
221 lines (190 loc) · 8.25 KB
/
run-GaMD.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
#!/bin/bash
echo "
#####################################################################
# GLOW version 1.0 #
# GLOW - GaMD, Deep Learning, Free Energy Profiling Workflow #
# Authors: Hung Do, Jinan Wang, Apurba Bhattarai, Yinglong Miao #
# Update in 10/2021 #
#===================================================================#
If you use any parts of GLOW, please cite: #
Do, H., Wang, J., Bhattarai, A., and Miao, Y. (2021). GLOW - a #
Workflow Integrating Gaussian accelerated Molecular Dynamics #
and Deep Learning for Free Energy Profiling. #
#####################################################################"
echo "
=====================================================================
IMPORTANT NOTES FOR USERS:
The input file must be named: GLOW.in
In GLOW.in, please keep the format of the variables as follows,
in case you have more systems, i.e.
- workfolder_1, workfolder_2, workfolder_3, ...
- parm_sys_1, parm_sys_2, parm_sys_3, ...
- nb_prot_1, nb_prot_2, nb_prot_3, ...
- ...
Please use CTRL + A & CTRL + D to log off your terminal!
If you run into any issues, please contact [email protected]
====================================================================="
parfolder=`pwd`
source $parfolder/GLOW.in
cd $parfolder
echo "Current Directory: $parfolder"
nb_systems=$nb_systems
echo "Number of systems: $nb_systems"
echo "
#####################################################################
# (I) GaMD - Gaussian accelerated Molecular Dynamics! #
#####################################################################"
echo "Set up your system with CHARMM-GUI and run the cMD beforehand!"
source ${AMBER}/amber.sh
echo "
=====================================================================
# Part 1.1: GaMD #
====================================================================="
echo "Your workstation must have $nb_systems GPUs"
echo "
Preparing GaMD Equilibration and Production Input Files"
for i in `seq 1 $nb_systems`
do
workfolder=workfolder_$i
parm_sys=parm_sys_$i
nb_protein=nb_prot_$i
rst_sys=rst_sys_$i
rst_full=${!rst_sys}
cuda_device=$(expr $i - 1)
work_dir=${!workfolder}
parm_full=${!parm_sys}
nb_prot=${!nb_protein}
natom_sys=`head -7 ${work_dir}/${parm_full} |tail -1 |awk '{print \$1}'`
ntave=`echo $((4000*(natom_sys/1000+1)))`
ntcmd=`echo $((ntave*5))`
ntcmdprep=`echo $((ntave*2))`
ntebprep=`echo $((ntave*2))`
nteb=`echo $((ntave*25))`
nstlim=`echo $((ntcmd+nteb))`
# echo ${natom_sys},${ntave},${ntcmd},${ntcmdprep},${ntebprep},${nteb},${nstlim}
echo "The directory for system $i is $work_dir"
mkdir -p $work_dir
rm $work_dir/md.in
echo "GaMD equilibration
&cntrl
imin=0, ! No minimization
irest=0, ! This IS a new MD simulation
ntx=1, ! read coordinates only
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
tempi=310.0, ! Initial temperature
temp0=310.0, ! Target temperature
ig=-1, ! random seed
! Potential energy control
cut=9.0, ! nonbonded cutoff, in Angstroms
! MD settings
nstlim=${nstlim}, ! simulation length
dt=0.002, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=2, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=500, ! Print energies every 500 steps
ntwx=500, ! Print coordinates every 500 steps to the trajectory
ntwr=10000, ! Print a restart file every 10K steps (can be less frequent)
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
ntwprt = $nb_prot,
! Constant pressure control. Note that ntp=3 requires barostat=1
barostat=1, ! Berendsen... change to 2 for MC barostat
ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
pres0=1.0, ! Target external pressure, in bar
taup=0.5, ! Berendsen coupling constant (ps)
! Constant surface tension (needed for semi-isotropic scaling). Uncomment
! for this feature. csurften must be nonzero if ntp=3 above
csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
ninterface=2, ! Number of interfaces (2 for bilayer)
! Set water atom/residue names for SETTLE recognition
watnam='WAT', ! Water residues are named TIP3
owtnm='O', ! Water oxygens are named OH2
! GaMD parameters
igamd = 3, iE = 1, irest_gamd = 0,
ntcmd = ${ntcmd}, nteb = ${nteb}, ntave = ${ntave},
ntcmdprep = ${ntcmdprep}, ntebprep = ${ntebprep},
sigma0P = 6.0, sigma0D = 6.0,
/" > $work_dir/md.in
rm $work_dir/gamd-restart.in
echo "GaMD simulation
&cntrl
imin=0, ! No minimization
irest=0, ! This IS a new MD simulation
ntx=1, ! read coordinates only
! Temperature control
ntt=3, ! Langevin dynamics
gamma_ln=1.0, ! Friction coefficient (ps^-1)
tempi=310.0, ! Initial temperature
temp0=310.0, ! Target temperature
ig=-1, ! random seed
! Potential energy control
cut=9.0, ! nonbonded cutoff, in Angstroms
! MD settings
nstlim=${total_prod_steps}, ! simulation length
dt=0.002, ! time step (ps)
! SHAKE
ntc=2, ! Constrain bonds containing hydrogen
ntf=2, ! Do not calculate forces of bonds containing hydrogen
! Control how often information is printed
ntpr=500, ! Print energies every 500 steps
ntwx=500, ! Print coordinates every 500 steps to the trajectory
ntwr=10000, ! Print a restart file every 10K steps (can be less frequent)
! ntwv=-1, ! Uncomment to also print velocities to trajectory
! ntwf=-1, ! Uncomment to also print forces to trajectory
ntxo=2, ! Write NetCDF format
ioutfm=1, ! Write NetCDF format (always do this!)
! Wrap coordinates when printing them to the same unit cell
iwrap=1,
ntwprt = $nb_prot,
! Constant pressure control. Note that ntp=3 requires barostat=1
barostat=1, ! Berendsen... change to 2 for MC barostat
ntp=3, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/ surften
pres0=1.0, ! Target external pressure, in bar
taup=0.5, ! Berendsen coupling constant (ps)
! Constant surface tension (needed for semi-isotropic scaling). Uncomment
! for this feature. csurften must be nonzero if ntp=3 above
csurften=3, ! Interfaces in 1=yz plane, 2=xz plane, 3=xy plane
gamma_ten=0.0, ! Surface tension (dyne/cm). 0 gives pure semi-iso scaling
ninterface=2, ! Number of interfaces (2 for bilayer)
! Set water atom/residue names for SETTLE recognition
watnam='WAT', ! Water residues are named TIP3
owtnm='O', ! Water oxygens are named OH2
! GaMD parameters
igamd = 3, iE = 1, irest_gamd = 1,
ntcmd = 0, nteb = 0, ntave = ${ntave},
ntcmdprep = 0, ntebprep = 0,
sigma0P = 6.0, sigma0D = 6.0,
/" > $work_dir/gamd-restart.in
rm $work_dir/run-gamd.sh
echo "export CUDA_VISIBLE_DEVICES=$cuda_device
cd $work_dir
pmemd.cuda -O -i md.in -p ${parm_full} -c ${rst_full} -o md-1.out -x md-1.nc -r md-1.rst -gamd gamd-1.log
pmemd.cuda -O -i gamd-restart.in -p $parm_full -c md-1.rst -o md-2.out -x md-2.nc -r gamd-2.rst -gamd gamd-2.log" > $work_dir/run-gamd.sh
echo "GaMD-$i is about to be run!"
if [ $i -lt $nb_systems ]
then
echo "GaMD-$i is running!"
sh $work_dir/run-gamd.sh &
if [ $? != 0 ]; then
echo "Errors with GaMD-$i!"
exit 0
fi
else
echo "GaMD-$i is running!"
sh $work_dir/run-gamd.sh
if [ $? != 0 ]; then
echo "Errors with GaMD-$i!"
exit 0
fi
fi
done
echo "GaMD's are done running!"