[AMBER] Explicit-solvent-pH-REMD

From: whb <wwwhbpt.gmail.com>
Date: Fri, 31 Jul 2015 15:48:28 +0800

Dear all

         When I restarted the pH-REMD simulation, Ií»ve got a problem about
the temperature, it fell soon from 300K to 4K.

At first it runs well when I restarted from the equilibrium step(runs in
different pH, but did not exchange pH protonation with each other).And the
temperature jumps between 260K to 300K, and Ií»ve accepted Jasoní»s
explanation ití»s the reason that the protein was frozen sometimes, and the
temp seems a bit lower.

I collected 10ns in the first simulation with Expilict solvent pH-REMD, it
seems well in VMD.

But when I want to restart this simulation using the same input file, the
temp fell soon from 300K to 4K.

I doní»t know what the problem is and I need your help!

Hereí»s my test input(record every stepí»s temp).

         Explicit solvent constant pH MD

       &cntrl

   imin=0, irest=1, ntx=5, ntxo=2,

   ntpr=1, ntwx=1,ntwr=1,nstlim=100,numexchg=10

   dt=0.002, ntt=3, tempi=300,

   temp0=300, gamma_ln=1.0, ig=-1,

   ntc=2, ntf=2, cut=10, iwrap=1,

   ioutfm=1, icnstph=2, ntcnstph=100,

   solvph=XXXXX, ntrelax=100, saltcon=0.1,

/

 

Hereis my output

NSTEP = 1 TIME(PS) = 15400.002 TEMP(K) = 298.71 PRESS =
0.0

Etot = -42194.6833 EKtot = 10969.1536 EPtot =
-53163.8368

BOND = 489.7344 ANGLE = 1373.1680 DIHED =
1822.0089

1-4 NB = 562.6703 1-4 EEL = 8404.9926 VDWAALS =
5802.5447

EELEC = -71618.9557 EHBOND = 0.0000 RESTRAINT =
0.0000

Ewald error estimate: 0.9809E-04

SOLVPH = 1.5000 REPNUM = 1 EXCHANGE# =
1

----------------------------------------------------------------------------
--
NSTEP =     1000   TIME(PS) =   15402.000  TEMP(K) =    26.47  PRESS =
0.0
Etot   =    -66318.1304  EKtot   =       972.0089  EPtot      =
-67290.1393
BOND   =       136.2482  ANGLE   =       556.4427  DIHED      =
1569.4363
1-4 NB =       499.3078  1-4 EEL =      7744.8644  VDWAALS    =
8674.4357
EELEC  =    -86470.8743  EHBOND  =         0.0000  RESTRAINT  =
0.0000
Ewald error estimate:   0.4960E-02
SOLVPH =         6.0000  REPNUM  =              1  EXCHANGE#  =
10
----------------------------------------------------------------------------
--
 
Haobo Wang
BNMRC 
CCME.PKU
TELú║13366116732
 
 
 
 
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Received on Fri Jul 31 2015 - 01:00:02 PDT
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