Hi Carlos,
Thank you for your prompt reply.
Your suggestion works.
Although I have read the methods of the following article carefully, I am still not confident with the parameters setting for my large protein systems.
I would appreciate it if you could give me the ".in" files for NEB four steps in Amber (1heat.in, 2equil, 3anneal.in, 4cool.in).
Then I could have a deep understanding of NEB.
Free Energy Landscapes for RBD Opening in SARS-CoV-2 Spike Glycoprotein
Simulations Suggest Key Interactions and a Potentially Druggable Allosteric
Pocket. <
https://doi.org/10.26434/chemrxiv.13502646> Lucy Fallon, Kellon
Belfon, Lauren Raguette, Yuzhang Wang, Christopher Corbo, Darya Stepanenko,
Abbigayle Cuomo, Jose Guerra, Stephanie Budhan, Sarah Varghese, Robert
Rizzo, Carlos Simmerling, *preprint*
Best wishes,
Pineapple
发件人: "Carlos Simmerling" <carlos.simmerling.gmail.com>
收件人: "amber" <amber.ambermd.org>
发送时间: 星期三, 2021年 2 月 03日 下午 9:17:30
主题: Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem
The first thing you should do is to turn on shake (ntc). is there a reason
it is off? Explicit water models are usually rigid and require shake.
then see how things go. You might want to look at other papers with
explicit solvent NEB, our lab has published several, a few are listed below.
Free Energy Landscapes for RBD Opening in SARS-CoV-2 Spike Glycoprotein
Simulations Suggest Key Interactions and a Potentially Druggable Allosteric
Pocket. <
https://doi.org/10.26434/chemrxiv.13502646> Lucy Fallon, Kellon
Belfon, Lauren Raguette, Yuzhang Wang, Christopher Corbo, Darya Stepanenko,
Abbigayle Cuomo, Jose Guerra, Stephanie Budhan, Sarah Varghese, Robert
Rizzo, Carlos Simmerling, *preprint*
*DNA Deformation-Coupled Recognition of 8‑Oxoguanine: Conformational
Kinetic Gating in Human DNA Glycosylase
<
https://doi.org/10.1021/jacs.6b11433>. Li, H., Endutkin, A., Bergonzo, C.,
Fu, L., Grollman, A., Zharkov, D., Simmerling, C., Journal of the American
Chemical Society, 2017, 139 (7), 2682-2692*
*Rational modulation of the induced-fit conformational change for
slow-onset inhibition in M. tuberculosis InhA
<
https://doi.org/10.1021/acs.biochem.5b00284>. Lai, C-T., Li, H; Yu, W.,
Shah, S., Bommineni, G., Perrone, V., Garcia-Diaz, M., Tonge, P.,
Simmerling, C., Biochemistry, 2015, 54 (30), 4683-4691*
On Wed, Feb 3, 2021 at 7:13 AM 李明玉 <santaclaus.sjtu.edu.cn> wrote:
> 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 - 09:30:02 PST
