Hello, I did REMD according to the tutorial. After the simulation is over, an error is reported when using ˇ° extract_300k_traj.xˇ± script to extract the temperature trajectory:
NETCDF file:
WARNING: setupREMDTRAJ(): remdtraj requested in trajin but this NETCDF trajectory does not contain temperatures! Trajectory will be processed as replica traj.
The ˇ°extract_300k_traj.xˇ± script is as follows:
#!/bin/csh
ptraj 5EK4_1.prmtop << EOF
trajin remd.mdcrd.001 remdtraj remdtrajtemp 300
trajout remd.300K.mdcrd nobox
go
EOF
The following are the key input files when I perform REMD:
remd.mdin:
&cntrl
irest=0, ntx=1,
nstlim=500, dt=0.002,
irest=0, ntt=3, gamma_ln=1.0,
temp0=XXXXX, ig=RANDOM_NUMBER,
ntc=2, ntf=2, nscm=1000,
ntb=0, igb=5,
cut=999.0, rgbmax=999.0,
ntpr=100, ntwx=1000, ntwr=10000,
nmropt=1,
numexchg=50000,
ntr=1,
restraint_wt=50.0,
restraintmask=':1-347,374-390.CA',
/
&wt TYPE='END'
/
DISANG=5EK4_chir.dat
REMD simulations are run for a temperature range between 290 - 472K. The starting structure of the 30 replicas of REMD is the 5EKC protein with 30 different structures. 50 ns for each replica.
remd.groupfile:
-O -rem 1 -remlog rem.log -i remd.mdin.001 -o remd.mdout.001 -c 5EK4_1.inpcrd -r remd.rst.001 -x remd.mdcrd.001 -inf remd.mdinfo.001 -p 5EK4_1.prmtop -ref 5EK4_1.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.002 -o remd.mdout.002 -c 5EK4_2.inpcrd -r remd.rst.002 -x remd.mdcrd.002 -inf remd.mdinfo.002 -p 5EK4_1.prmtop -ref 5EK4_2.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.003 -o remd.mdout.003 -c 5EK4_3.inpcrd -r remd.rst.003 -x remd.mdcrd.003 -inf remd.mdinfo.003 -p 5EK4_1.prmtop -ref 5EK4_3.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.004 -o remd.mdout.004 -c 5EK4_4.inpcrd -r remd.rst.004 -x remd.mdcrd.004 -inf remd.mdinfo.004 -p 5EK4_1.prmtop -ref 5EK4_4.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.005 -o remd.mdout.005 -c 5EK4_5.inpcrd -r remd.rst.005 -x remd.mdcrd.005 -inf remd.mdinfo.005 -p 5EK4_1.prmtop -ref 5EK4_5.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.006 -o remd.mdout.006 -c 5EK4_6.inpcrd -r remd.rst.006 -x remd.mdcrd.006 -inf remd.mdinfo.006 -p 5EK4_1.prmtop -ref 5EK4_6.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.007 -o remd.mdout.007 -c 5EK4_7.inpcrd -r remd.rst.007 -x remd.mdcrd.007 -inf remd.mdinfo.007 -p 5EK4_1.prmtop -ref 5EK4_7.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.008 -o remd.mdout.008 -c 5EK4_8.inpcrd -r remd.rst.008 -x remd.mdcrd.008 -inf remd.mdinfo.008 -p 5EK4_1.prmtop -ref 5EK4_8.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.009 -o remd.mdout.009 -c 5EK4_9.inpcrd -r remd.rst.009 -x remd.mdcrd.009 -inf remd.mdinfo.009 -p 5EK4_1.prmtop -ref 5EK4_9.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.010 -o remd.mdout.010 -c 5EK4_10.inpcrd -r remd.rst.010 -x remd.mdcrd.010 -inf remd.mdinfo.010 -p 5EK4_1.prmtop -ref 5EK4_10.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.011 -o remd.mdout.011 -c 5EK4_11.inpcrd -r remd.rst.011 -x remd.mdcrd.011 -inf remd.mdinfo.011 -p 5EK4_1.prmtop -ref 5EK4_11.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.012 -o remd.mdout.012 -c 5EK4_12.inpcrd -r remd.rst.012 -x remd.mdcrd.012 -inf remd.mdinfo.012 -p 5EK4_1.prmtop -ref 5EK4_12.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.013 -o remd.mdout.013 -c 5EK4_13.inpcrd -r remd.rst.013 -x remd.mdcrd.013 -inf remd.mdinfo.013 -p 5EK4_1.prmtop -ref 5EK4_13.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.014 -o remd.mdout.014 -c 5EK4_14.inpcrd -r remd.rst.014 -x remd.mdcrd.014 -inf remd.mdinfo.014 -p 5EK4_1.prmtop -ref 5EK4_14.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.015 -o remd.mdout.015 -c 5EK4_15.inpcrd -r remd.rst.015 -x remd.mdcrd.015 -inf remd.mdinfo.015 -p 5EK4_1.prmtop -ref 5EK4_15.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.016 -o remd.mdout.016 -c 5EK4_16.inpcrd -r remd.rst.016 -x remd.mdcrd.016 -inf remd.mdinfo.016 -p 5EK4_1.prmtop -ref 5EK4_16.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.017 -o remd.mdout.017 -c 5EK4_17.inpcrd -r remd.rst.017 -x remd.mdcrd.017 -inf remd.mdinfo.017 -p 5EK4_1.prmtop -ref 5EK4_17.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.018 -o remd.mdout.018 -c 5EK4_18.inpcrd -r remd.rst.018 -x remd.mdcrd.018 -inf remd.mdinfo.018 -p 5EK4_1.prmtop -ref 5EK4_18.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.019 -o remd.mdout.019 -c 5EK4_19.inpcrd -r remd.rst.019 -x remd.mdcrd.019 -inf remd.mdinfo.019 -p 5EK4_1.prmtop -ref 5EK4_19.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.020 -o remd.mdout.020 -c 5EK4_20.inpcrd -r remd.rst.020 -x remd.mdcrd.020 -inf remd.mdinfo.020 -p 5EK4_1.prmtop -ref 5EK4_20.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.021 -o remd.mdout.021 -c 5EK4_21.inpcrd -r remd.rst.021 -x remd.mdcrd.021 -inf remd.mdinfo.021 -p 5EK4_1.prmtop -ref 5EK4_21.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.022 -o remd.mdout.022 -c 5EK4_22.inpcrd -r remd.rst.022 -x remd.mdcrd.022 -inf remd.mdinfo.022 -p 5EK4_1.prmtop -ref 5EK4_22.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.023 -o remd.mdout.023 -c 5EK4_23.inpcrd -r remd.rst.023 -x remd.mdcrd.023 -inf remd.mdinfo.023 -p 5EK4_1.prmtop -ref 5EK4_23.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.024 -o remd.mdout.024 -c 5EK4_24.inpcrd -r remd.rst.024 -x remd.mdcrd.024 -inf remd.mdinfo.024 -p 5EK4_1.prmtop -ref 5EK4_24.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.025 -o remd.mdout.025 -c 5EK4_25.inpcrd -r remd.rst.025 -x remd.mdcrd.025 -inf remd.mdinfo.025 -p 5EK4_1.prmtop -ref 5EK4_25.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.026 -o remd.mdout.026 -c 5EK4_26.inpcrd -r remd.rst.026 -x remd.mdcrd.026 -inf remd.mdinfo.026 -p 5EK4_1.prmtop -ref 5EK4_26.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.027 -o remd.mdout.027 -c 5EK4_27.inpcrd -r remd.rst.027 -x remd.mdcrd.027 -inf remd.mdinfo.027 -p 5EK4_1.prmtop -ref 5EK4_27.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.028 -o remd.mdout.028 -c 5EK4_28.inpcrd -r remd.rst.028 -x remd.mdcrd.028 -inf remd.mdinfo.028 -p 5EK4_1.prmtop -ref 5EK4_28.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.029 -o remd.mdout.029 -c 5EK4_29.inpcrd -r remd.rst.029 -x remd.mdcrd.029 -inf remd.mdinfo.029 -p 5EK4_1.prmtop -ref 5EK4_29.inpcrd
-O -rem 1 -remlog rem.log -i remd.mdin.030 -o remd.mdout.030 -c 5EK4_30.inpcrd -r remd.rst.030 -x remd.mdcrd.030 -inf remd.mdinfo.030 -p 5EK4_1.prmtop -ref 5EK4_30.inpcrd
The command to run REMD is:
srun -n 30 pmemd.cuda.MPI -ng 30 -groupfile remd.groupfile
The output file is as follows:
rem.log:
.........
# exchange 50000
1 -1.00 483.93 -4919.86 472.00 472.00 0.00 -1
2 1.01 425.03 -5615.09 421.90 428.80 0.28 -1
3 -1.00 357.92 -6665.98 363.30 363.30 0.26 -1
4 -1.00 431.49 -5213.03 443.00 443.00 0.29 -1
5 0.99 310.04 -7672.94 316.80 311.30 0.25 -1
6 -1.00 381.14 -6215.04 395.00 395.00 0.27 -1
7 0.99 457.53 -5069.34 457.60 450.20 0.29 -1
8 0.99 308.95 -7850.23 305.80 300.50 0.24 -1
9 1.01 310.87 -7623.60 311.30 316.80 0.25 -1
10 -1.00 435.48 -5500.29 435.90 435.90 0.29 -1
11 0.99 422.83 -5597.49 428.80 421.90 0.28 -1
12 -1.00 320.61 -7401.61 322.30 322.30 0.25 -1
13 1.01 448.75 -5117.91 450.20 457.60 0.28 -1
14 1.01 300.06 -7902.66 300.50 305.80 0.25 -1
15 -1.00 407.83 -6045.13 401.60 401.60 0.27 -1
16 -1.00 411.97 -5993.03 408.30 408.30 0.28 -1
17 -1.00 342.54 -7093.49 345.30 345.30 0.26 -1
18 -1.00 374.51 -6618.57 369.50 369.50 0.27 -1
19 -1.00 406.04 -5767.74 415.00 415.00 0.28 -1
20 -1.00 347.37 -7103.56 339.40 339.40 0.26 -1
21 -1.00 328.74 -7117.47 333.60 333.60 0.25 -1
22 -1.00 354.91 -6798.13 357.20 357.20 0.26 -1
23 -1.00 377.97 -6340.68 382.10 382.10 0.28 -1
24 0.99 294.19 -7967.01 295.20 290.00 0.25 -1
25 1.01 291.39 -7976.23 290.00 295.20 0.25 -1
26 -1.00 326.46 -7318.99 327.90 327.90 0.25 -1
27 -1.00 380.62 -6394.33 375.70 375.70 0.26 -1
28 -1.00 384.89 -6096.66 388.50 388.50 0.28 -1
29 -1.00 349.34 -6909.41 351.20 351.20 0.26 -1
30 -1.00 468.11 -5049.65 465.00 465.00 0.32 -1
remd.mdout.010 :
........
===============================================================================
NSTEP = 24999800 TIME(PS) = 49999.600 TEMP(K) = 439.90 PRESS = 0.0
Etot = 1470.6336 EKtot = 6895.8413 EPtot = -5425.2077
BOND = 1745.3514 ANGLE = 4394.8278 DIHED = 5328.6671
1-4 NB = 1544.8450 1-4 EEL = 17601.7434 VDWAALS = -3226.1926
EELEC = -28591.7114 EGB = -4559.0270 RESTRAINT = 336.2887
EAMBER (non-restraint) = -5761.4964
TEMP0 = 435.9000 REPNUM = 10 EXCHANGE# = 50000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 19.562
===============================================================================
NSTEP = 24999900 TIME(PS) = 49999.800 TEMP(K) = 432.41 PRESS = 0.0
Etot = 1350.3298 EKtot = 6778.4297 EPtot = -5428.0999
BOND = 1729.3050 ANGLE = 4370.8293 DIHED = 5383.2636
1-4 NB = 1566.0495 1-4 EEL = 17505.5943 VDWAALS = -3259.0800
EELEC = -28657.4152 EGB = -4427.6502 RESTRAINT = 361.0038
EAMBER (non-restraint) = -5789.1037
TEMP0 = 435.9000 REPNUM = 10 EXCHANGE# = 50000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 21.718
===============================================================================
NSTEP = 25000000 TIME(PS) = 50000.000 TEMP(K) = 433.81 PRESS = 0.0
Etot = 1429.7036 EKtot = 6800.4443 EPtot = -5370.7407
BOND = 1641.3302 ANGLE = 4534.2074 DIHED = 5377.9737
1-4 NB = 1573.3763 1-4 EEL = 17498.4438 VDWAALS = -3220.7094
EELEC = -28666.4125 EGB = -4444.1999 RESTRAINT = 335.2497
EAMBER (non-restraint) = -5705.9904
TEMP0 = 435.9000 REPNUM = 10 EXCHANGE# = 50000
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 18.340
===============================================================================
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Received on Thu Apr 15 2021 - 20:00:02 PDT
