Hi Amber users,
I am trying to perform nudged elastic band method (NEB) on a large 1618-residue protein.
I am using the same NEB parameters and protocol as the Amber tutorial A5, except for those relating to implicit solvent. Here, I applied the explicit solvent. All the initial structures have been carefully prepared and minimized.
However, when I checked the output of the initial heating MD, the individual replicate energies were **** (change the cut to 9999 also cause this problem).
Please see the output 1 below.
Then I tried NEB with implicit solvent , adopting the same parameter as the tutorial, the energy problem seems to be solved.
I found the energy of this system was small without plenty of solvent-solvent interactions. That may be the reason to solve the problem.
Please see the output 2 below.
Therefore, I have the following questions:
For large protein systems, what is the best type of solvent to choose?
In my opinion, although there are lots of solvent-solvent interactions, the explicit solvent would still be better since it is close to the reality.
If so, how to solve the initial heating problems with the explicit solvent?
My opinion might be ill-considered for I'm new to MD.
Any suggestions on what I might have done wrong would be much appreciated.
Many thanks,
Pineapple
Output1:
-------------------------------------------------------
Amber 18 PMEMD 2018
-------------------------------------------------------
Here is the input file:
&cntrl
imin = 0, irest = 0,
ntc=1, ntf=1,
ntpr=1000, ntwx=10000,
ntb = 1, igb=0, cut=10, rgbmax=10,
nstlim = 1000000, nscm=0,
dt = 0.0005, ig=-1,
ntt = 3, gamma_ln=1000.0,
tempi=0.0, temp0=300.0,
tgtfitmask=":1-1618.CA",
tgtrmsmask=":1-1618",
ineb = 1,skmin = 10,skmax = 10,
nmropt=1,
/
&wt type='TEMP0', istep1=0,istep2=800000,
value1=0.0, value2=300.0
/
&wt type='END'
/
|------------------- GPU DEVICE INFO --------------------
|
| Task ID: 0
| CUDA_VISIBLE_DEVICES: 0,1,2,3,4,5,6,7
| CUDA Capable Devices Detected: 8
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla V100-SXM2-16GB
| CUDA Device Global Mem Size: 16130 MB
| CUDA Device Num Multiprocessors: 80
| CUDA Device Core Freq: 1.53 GHz
|
|--------------------------------------------------------
|---------------- GPU PEER TO PEER INFO -----------------
|
| Peer to Peer support: ENABLED
|
|--------------------------------------------------------
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
The following selection will be used for NEB structure fitting
Mask ":1-1618.CA" matches 1618 atoms
The following selection will be used for NEB force application
Mask ":1-1618" matches 25494 atoms
Last atom in NEB fitmask or rmsmask is 25494
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -686665.5046 EKtot = 0.0000 EPtot = -686665.5046
BOND = 49737.9500 ANGLE = 16906.3886 DIHED = 21361.6559
1-4 NB = 74233.0973 1-4 EEL = 74040.2101 VDWAALS = 69345.1204
EELEC = -992289.9269 EHBOND = 0.0000 RESTRAINT = 0.0000
NEB replicate breakdown:
Energy for replicate 1 = -686665.5046
Energy for replicate 2 = -686665.5046
Energy for replicate 3 = -686665.5046
Energy for replicate 4 = -686665.5046
Energy for replicate 5 = -686665.5046
Energy for replicate 6 = -686665.5046
Energy for replicate 7 = -686665.5046
Energy for replicate 8 = -686665.5046
Energy for replicate 9 = -686665.5046
Energy for replicate 10 = -686665.5046
Energy for replicate 11 = -686665.5046
Energy for replicate 12 = -686665.5046
Energy for replicate 13 = -686665.5046
Energy for replicate 14 = -686665.5046
Energy for replicate 15 = -686665.5046
Energy for replicate 16 = -686665.5046
Energy for replicate 17 = -543804.4518
Energy for replicate 18 = -543804.4518
Energy for replicate 19 = -543804.4518
Energy for replicate 20 = -543804.4518
Energy for replicate 21 = -543804.4518
Energy for replicate 22 = -543804.4518
Energy for replicate 23 = -543804.4518
Energy for replicate 24 = -543804.4518
Energy for replicate 25 = -543804.4518
Energy for replicate 26 = -543804.4518
Energy for replicate 27 = -543804.4518
Energy for replicate 28 = -543804.4518
Energy for replicate 29 = -543804.4518
Energy for replicate 30 = -543804.4518
Energy for replicate 31 = -543804.4518
Energy for replicate 32 = -543804.4518
Total Energy of replicates = *************
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 1000 TIME(PS) = 0.500 TEMP(K) = 0.00 PRESS = 0.0
Etot = -686665.5046 EKtot = 0.0000 EPtot = -686665.5046
BOND = 49737.9500 ANGLE = 16906.3886 DIHED = 21361.6559
1-4 NB = 74233.0973 1-4 EEL = 74040.2101 VDWAALS = 69345.1204
EELEC = -992289.9269 EHBOND = 0.0000 RESTRAINT = 0.0000
NEB replicate breakdown:
Energy for replicate 1 = -686665.5046
Energy for replicate 2 = *************
Energy for replicate 3 = *************
Energy for replicate 4 = *************
Energy for replicate 5 = *************
Energy for replicate 6 = *************
Energy for replicate 7 = *************
Energy for replicate 8 = *************
Energy for replicate 9 = *************
Energy for replicate 10 = *************
Energy for replicate 11 = *************
Energy for replicate 12 = *************
Energy for replicate 13 = *************
Energy for replicate 14 = *************
Energy for replicate 15 = *************
Energy for replicate 16 = *************
Energy for replicate 17 = *************
Energy for replicate 18 = *************
Energy for replicate 19 = *************
Energy for replicate 20 = *************
Energy for replicate 21 = *************
Energy for replicate 22 = *************
Energy for replicate 23 = *************
Energy for replicate 24 = *************
Energy for replicate 25 = *************
Energy for replicate 26 = *************
Energy for replicate 27 = *************
Energy for replicate 28 = *************
Energy for replicate 29 = *************
Energy for replicate 30 = *************
Energy for replicate 31 = *************
Energy for replicate 32 = -543804.4518
Total Energy of replicates = *************
------------------------------------------------------------------------------
Output2:
Here is the input file:
&cntrl
imin = 0, irest = 0,
ntc=1, ntf=1,
ntpr=1000, ntwx=10000,
ntb = 0, cut = 999.0, rgbmax=999.0,
igb = 1, saltcon=0.2,
nstlim = 1000000, nscm=0,
dt = 0.0005, ig=-1,
ntt = 3, gamma_ln=1000.0,
tempi=0.0, temp0=300.0,
tgtfitmask=":1-1618.CA",
tgtrmsmask=":1-1618",
ineb = 1,skmin = 10,skmax = 10,
nmropt=1,
/
&wt type='TEMP0', istep1=0,istep2=800000,
value1=0.0, value2=300.0
/
&wt type='END'
/
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
The following selection will be used for NEB structure fitting
Mask ":1-1618.CA" matches 1618 atoms
The following selection will be used for NEB force application
Mask ":1-1618" matches 25494 atoms
Last atom in NEB fitmask or rmsmask is 25494
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -47074.9209 EKtot = 0.0000 EPtot = -47074.9209
BOND = 970.8273 ANGLE = 3662.2135 DIHED = 19095.3704
1-4 NB = 5347.5040 1-4 EEL = 70022.7257 VDWAALS = -12763.4042
EELEC = -116272.6746 EGB = -17137.4828 RESTRAINT = 0.0000
NEB replicate breakdown:
Energy for replicate 1 = -47074.9209
Energy for replicate 2 = -47074.9209
Energy for replicate 3 = -47074.9209
Energy for replicate 4 = -47074.9209
Energy for replicate 5 = -47074.9209
Energy for replicate 6 = -47074.9209
Energy for replicate 7 = -47074.9209
Energy for replicate 8 = -47074.9209
Energy for replicate 9 = -47074.9209
Energy for replicate 10 = -47074.9209
Energy for replicate 11 = -47074.9209
Energy for replicate 12 = -47074.9209
Energy for replicate 13 = -47074.9209
Energy for replicate 14 = -47074.9209
Energy for replicate 15 = -47074.9209
Energy for replicate 16 = -47074.9209
Energy for replicate 17 = -47224.1291
Energy for replicate 18 = -47224.1291
Energy for replicate 19 = -47224.1291
Energy for replicate 20 = -47224.1291
Energy for replicate 21 = -47224.1291
Energy for replicate 22 = -47224.1291
Energy for replicate 23 = -47224.1291
Energy for replicate 24 = -47224.1291
Energy for replicate 25 = -47224.1291
Energy for replicate 26 = -47224.1291
Energy for replicate 27 = -47224.1291
Energy for replicate 28 = -47224.1291
Energy for replicate 29 = -47224.1291
Energy for replicate 30 = -47224.1291
Energy for replicate 31 = -47224.1291
Energy for replicate 32 = -47224.1291
Total Energy of replicates = -1508784.8001
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 1000 TIME(PS) = 0.500 TEMP(K) = 0.00 PRESS = 0.0
Etot = -47074.9209 EKtot = 0.0000 EPtot = -47074.9209
BOND = 970.8273 ANGLE = 3662.2135 DIHED = 19095.3704
1-4 NB = 5347.5040 1-4 EEL = 70022.7257 VDWAALS = -12763.4042
EELEC = -116272.6746 EGB = -17137.4828 RESTRAINT = 0.0000
NEB replicate breakdown:
Energy for replicate 1 = -47074.9209
Energy for replicate 2 = -47338.7714
Energy for replicate 3 = -47452.8556
Energy for replicate 4 = -47523.3896
Energy for replicate 5 = -47567.5181
Energy for replicate 6 = -47593.6794
Energy for replicate 7 = -47607.9944
Energy for replicate 8 = -47616.0892
Energy for replicate 9 = -47621.0239
Energy for replicate 10 = -47623.2967
Energy for replicate 11 = -47626.3209
Energy for replicate 12 = -47606.0063
Energy for replicate 13 = -47301.0893
Energy for replicate 14 = -43986.1754
Energy for replicate 15 = -9617.2634
Energy for replicate 16 = 160468.8020
Energy for replicate 17 = 161919.1912
Energy for replicate 18 = -8970.7711
Energy for replicate 19 = -43988.7678
Energy for replicate 20 = -47409.1935
Energy for replicate 21 = -47717.8482
Energy for replicate 22 = -47741.0225
Energy for replicate 23 = -47738.2980
Energy for replicate 24 = -47735.4112
Energy for replicate 25 = -47732.2131
Energy for replicate 26 = -47725.8105
Energy for replicate 27 = -47713.8208
Energy for replicate 28 = -47691.4394
Energy for replicate 29 = -47650.9497
Energy for replicate 30 = -47584.8315
Energy for replicate 31 = -47474.7247
Energy for replicate 32 = -47224.1291
Total Energy of replicates = -1020867.6326
------------------------------------------------------------------------------
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Received on Wed Feb 03 2021 - 04:30:02 PST
