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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 05 2014 - 03:30:02 PST
