[AMBER] Problems with implicit solvent

From: Carlo Guardiani <carlo.guardiani.dsf.unica.it>
Date: Fri, 5 Dec 2014 12:11:56 +0100

Dear Amber developers,
I am performing T-REMD simulations in implicit solvent (igb=7) of a
peptide using the CUDA version of Amber14 and the ff14SB force field. I
first performed a simulation using the default values of the internal and
external dielectric constants and I attained a certain secondary structure
profile. I then tried to repeat the simulation in a more hydrophobic
solvent lowering the extdiel parameter but I attained exactly the same
profile of secondary structure so that I believe that my command was
simply ignored. Here are the input files of the two simulations:

=======================================
WATER SIMULATION MDIN
=======================================

REMD
 &cntrl
   irest=0, ntx=1,
   nstlim=1250, dt=0.002,
   ntt=3, gamma_ln=1.0,
   temp0=300.00000000000000, ig=29600,
   ntc=2, ntf=2, nscm=1000,
   ntb=0, igb=7, saltcon=0.01,
   cut=999.0, rgbmax=999.0,
   ntpr=1250, ntwx=1250, ntwr=1250,
   numexchg=40000,
 /

==========================================
HYDROPHOBIC SOLVENT SIMULATION MDIN
==========================================

REMD
 &cntrl
   irest=0, ntx=1,
   nstlim=1250, dt=0.002,
   ntt=3, gamma_ln=1.0,
   temp0=300.00000000000000, ig=29600,
   ntc=2, ntf=2, nscm=1000,
   ntb=0, igb=7, saltcon=0.01,
   cut=999.0, rgbmax=999.0,
   ntpr=1250, ntwx=1250, ntwr=1250,
   numexchg=40000,
   intdiel=1.0, extdiel=26.7,
 /

The simulation in hydrophobic solvent seems to correctly read the input file
as shown by the content of the mdout files:

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

NMET

General flags:
     imin = 0, nmropt = 0

Replica exchange
     numexchg= 40000, rem= 1

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 1250, ntrx = 1, ntwr =
1250
     iwrap = 0, ntwx = 1250, ntwv = 0, ntwe =
   0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat=
   0

Potential function:
     ntf = 2, ntb = 0, igb = 7, nsnb =
  25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
     saltcon = 0.01000, offset = 0.09000, gbalpha= 1.09511
     gbbeta = 1.90793, gbgamma = 2.50798, surften = 0.00500
     rdt = 0.00000, rgbmax = 999.00000 extdiel = 26.70000
     alpb = 0


Following the suggestions on the manual, in both simulations the bondi
radii were used:

source leaprc.ff14SB
set default PBradii bondi
a=sequence {NMET CYS ILE PRO PRO SER TYR ALA ASP LEU GLY LYS ALA ALA ARG
ASP ILE PHE ASN LYS GLY PHE GLY PHE CGLY }
saveamberparm a vdac2.prmtop vdac2.inpcrd
savepdb a vdac2_xleap.pdb
quit

The programs have been run with the script:

#!/bin/bash
source /etc/modules.sh
module load intel openmpi amber14
export CUDA_VISIBLE_DEVICES=0,1,2,3
mpirun -np 20 pmemd.cuda.MPI -ng 20 -groupfile remd.groupfile


Did I make any mistake or is there any bug with the force field or the
Amber release I have used ?

Thank you very much for your help and kind regards,

Carlo Guardiani





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Received on Fri Dec 05 2014 - 03:30:02 PST
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