Dear Abhishek,
PMEMD does not support the polarizable force fields (other than amoeba
through a separate executable). See page 200 of the AMBER 10 manual which
lists what is an isn't supported in PMEMD:
ipol!=0 In &cntrl. Polarizable force field simulations are not supported,
other than amoeba,
which is supported in pmemd.amba.
You will need to use sander.MPI instead.
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Abhishek Singh
Sent: Thursday, July 03, 2008 7:54 AM
To: amber.scripps.edu
Subject: AMBER: PMEMD and polarized force field ff 02
Dear All
I have a situation that I am simulating rna molecule in a TIP3PBOX using
ff02 force field and salt libraries ionsjc_tip3p. While equilibration there
is a protocol PMEMD that has input file as shown below. Now if i use the
flag ipol=1 in all my sander input files the simulation crashes.
Now two options
1) I tried to skip this stage then got trouble when in last step of
minimization when i have no constrains on the RNA molecule.
2) if i turn off the flag igb=0 then it kills my periodic boundary
conditions of the solvation box.
Kindly suggest how can i run md without PME.
PMEMD input file is
heat/dynamics holding RNA fixed
&cntrl
imin=0,
ntxo=1, ntrx=1,
cut=9.0, tempi=100.0, ntwprt=0,
ntpr=100, ntwx=500, ntwe=500,
nstlim=10000, temp0=300.0,
nscm=0,nsnb=10,
ntc=2, ntf=2, tol=0.00001,
tautp=0.2, t=0.0, vlimit=20.0, comp=44.6,
ntx=1, irest=0, dielc=1.0, ibelly=0,
ntb=2, ntp=1, pres0=1.0, taup=0.2,
scee=1.2, dt=0.002,
ntt=1, ntr=1,ipol=1,
&end
GROUP FOR CONSTRAINTS
200.0
RES 1 32
END
END
With Regards,
Abhishek Singh
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Received on Sun Jul 06 2008 - 06:07:32 PDT
