Hi:
I have used NTP=2 in my constant pressure MD simulation of DMPC bilayer +
protein, however, with Sander using Amber8.
I did not find any problem, here is the input::
----------------------------------------------------------------------------
----------------------------------------------------------
&cntrl
imin = 0,
irest = 1,
ntx = 7,
ntb = 2,
ntp = 2,
pres0 = 1.0,
taup = 2.0,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
nstlim = 100000, dt = 0.002,
ntpr = 100, ntwx = 2000, ntwr = 1000
restraint_wt=50.0
restraintmask=':1-297.CA,C,O,N,H'
/
----------------------------------------------------------------------------
----------------------------------------------------------
Best, Akshay (Olemiss)
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Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Linda Prengaman
Sent: Friday, March 16, 2007 8:24 AM
To: amber.scripps.edu
Subject: AMBER: Problem with anisotropic pressure scaling
Dear Fellow AMBER Users:
I am trying to do a constant pressure MD run on a DMPC lipid bilayer. I
would like to set ntp=2, as that seems more appropriate for membrane
simulations. However, when I try to run the simulation, I get the following
error message in the output file:
Unit 5 Error on OPEN: lipid_only_constP_NTP.in
This is a pmemd run (amber7).
I also get the following error in the nohup.out file (I am using no hookup)
Unit 5 Error on OPEN: lipid_only_constP_NTP.in
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_11748: p4_error: : 1
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
Killed by signal 2.
/usr/local/mpich-1.2.4/bin/mpirun: line 1: 11748 Broken pipe
The exact same job with ntp=1 runs with no error message.
Here is the input file in question:
&cntrl
nstlim=100000,
imin=0,nscm=1000,
nmropt=0,
ntx=1,irest=0,ntrx=1,
ntxo=1,ntpr=500,ntwr=500,ntwx=500,ntwv=0,ntwe=0,iwrap=1,
ntf=2,ntc=2,dt=0.002,
scnb=8.0,scee=1.2,
cut=12,ntb=2,
ntp=2,taup=0.2,pres0=1.0,plevel=2,
ntt=1,temp0=100,tempi=3,ig=3455476,tautp=1.0
&end
Lipid Constraints
100.0
ATOM 1 5888
END
END
The box is orthogonal, so I don't understand what other problem there could
be. Please help.
Thank you,
Linda Prengaman
Department of Chemistry
Carnegie Mellon University
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Received on Sun Mar 18 2007 - 06:07:32 PDT
