# [AMBER] aMD used for simulated small peptide with non-standard residues

From: Gabriel Jara <gabriel.fcq.unc.ar.gmail.com>
Date: Mon, 24 Oct 2016 16:38:42 -0200

Dear all,

I am simulating a small peptide (four residues) that have non-standard
residue, so I parametrized them using R.E.D. Server Dev. In adittion, this
peptide is solvated by chloroform.

I am interested in performing a conformational sampling of the peptide in
order to know its preferential conformations. I think about use accelerated
molecular dynamics (aMD) for that.

Unfortunately, I have had problems in the aMD simulations in NVT conditions
at 243.14K. At the beginning the simulation looks good, although, the
temperature oscillates around 10K. However, then aprox. 100000 steps, the
simulation produce hugh values in potential and kinetics energies. The
structure of the system (peptide and solvente) colapse, forming a structure
completed distorted for peptide and solvent.

aMD parameters used in the simulation, simulation parameter input and
simulation printed output are at the end of the mail.

Could anyone help me or try to give a orientation about the problem?

does aMD apply to non-biological systems? (I did not find bibliography for
similar cases or in material simulations)

Gabriel

- Parameter and how I calculated are:

Average Dihedral : 87.9052 (based on MD simulations)
Average EPtot : -13042.6 (based on MD simulations)
total ATOMS=10166
protein residues=6

For the dihedral potential:
Approximate energy contribution per degree of freedom.
3.5*6= 21 The value of 3.5 kcal/mol/residue seems to work well

EthreshD = 21+87 = 109

alphaP = 10166*(1/5)=2033.2

EthreshP = -13042.6 + 2033.2 = -11009.4

- amber input simulation:

NVT
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000000,dt=0.002,
ntc=2, ntf=2, ig=-1,
cut=10.0, ntb=1, ntp=0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=243.15, ioutfm=1, iwrap=1,
iamd=3, EthreshD=122,
alphaP=2033.2,
/

- part of the output

NSTEP = 1296000 TIME(PS) = 522791.997 TEMP(K) = 247.60 PRESS =
0.0
Etot = -3785.3548 EKtot = 7483.4775 EPtot =
-11268.8323
BOND = 2739.1025 ANGLE = 3226.1308 DIHED =
124.0204
1-4 NB = 33.9589 1-4 EEL = 219.0100 VDWAALS =
-16929.3974
EELEC = -719.6022 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 37.9447
-----------------------------------------------------------
-------------------

wrapping first mol.: 63.60733 63.60538 -63.60441

NSTEP = 1297000 TIME(PS) = 522793.997 TEMP(K) = 252.18 PRESS =
0.0
Etot = -3786.6923 EKtot = 7622.0542 EPtot =
-11408.7465
BOND = 2582.2457 ANGLE = 3127.0807 DIHED =
110.1413
1-4 NB = 39.1142 1-4 EEL = 210.3087 VDWAALS =
-16875.5282
EELEC = -707.1741 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 105.0653
-----------------------------------------------------------
-------------------

wrapping first mol.: 63.60733 63.60538 -63.60441

NSTEP = 1298000 TIME(PS) = 522795.997 TEMP(K) = 248.28 PRESS =
0.0
Etot = -3849.2499 EKtot = 7504.1724 EPtot =
-11353.4223
BOND = 2643.6501 ANGLE = 3162.1880 DIHED =
117.2029
1-4 NB = 39.5800 1-4 EEL = 209.2930 VDWAALS =
-16900.8717
EELEC = -696.4797 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 72.0151
-----------------------------------------------------------
-------------------

wrapping first mol.: 63.60733 63.60538 -63.60441

NSTEP = 1299000 TIME(PS) = 522797.997 TEMP(K) = 255.47 PRESS =
0.0
Etot = -3605.1739 EKtot = 7721.3174 EPtot =
-11326.4913
BOND = 2637.9906 ANGLE = 3260.4554 DIHED =
129.4517
1-4 NB = 43.1732 1-4 EEL = 220.6721 VDWAALS =
-16960.8829
EELEC = -715.9414 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 58.5901
-----------------------------------------------------------
-------------------

wrapping first mol.: 298572.81211 1044527.59988 72699.83947

NSTEP = 1300000 TIME(PS) = 522799.997 TEMP(K) =********* PRESS =
0.0
Etot = ************** EKtot = ************** EPtot =
**************
BOND = ************** ANGLE = 878208.0714 DIHED =
793.0408
1-4 NB = 0.0000 1-4 EEL = -0.0001 VDWAALS =
**************
EELEC = -2270.5382 EHBOND = 0.0000 RESTRAINT =
0.0000
EAMD_BOOST = 0.0000
-----------------------------------------------------------
-------------------

```--
Dr. Gabriel E. Jara
Instituto de Química / UNICAMP
Rua Josué de Castro s/n
Cidade Universitária "Zeferino Vaz", Barão Geraldo
13083-861 Campinas, São Paulo, Brasil
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Received on Mon Oct 24 2016 - 12:00:02 PDT
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