Hi
I am doing simulation of a protein embedded in a membrane system. I
constructed the membrane system by CHARMM-GUI. Then I parameterized the
membrane system in leap as follows so:
LEAP
source leaprc.ff12SB
source leaprc.lipid11
source leaprc.gaff
loadamberparams ligand.params
lig=loadmol2 ligand.mol2
rec=loadpdb membran.pdb
com=combine {rec lig}
setBox com centers
saveamberparm com mol.prmtop mol.x
I minimized the structure using the following parameters:
relax.in
Minimize the lipid structure
&cntrl
imin=1,
maxcyc=10000,
ncyc=5000,
ntb=1,
ntp=0,
ntf=1,
ntc=1,
cut=10.0,
ntpr=50,
ntwr=2000,
ioutfm=1,
/
Then I heated the system in two step using the following parameters:
temp1.in
heating
&cntrl
imin=0, ntx=1, irest=0,
ntc=2, ntf=2, tol=0.0000001,
nstlim=2500, ntt=3, gamma_ln=1.0,
ntr=1, ig=-1,
ntpr=100, ntwr=10000, ntwx=100,
dt=0.002, nmropt=1,
ntb=1, ntp=0, cut=10.0, ioutfm=1,
/
&wt type='TEMP0', istep1=0, istep2=2500,
value1=0.0, value2=100.0 /
&wt type='END' /
Hold lipid fixed
10.0
RES 231 581
END
END
temp2.in
heating
&cntrl
imin=0, ntx=5, irest=1,
ntc=2, ntf=2,tol=0.0000001,
nstlim=50000, ntt=3, gamma_ln=1.0,
ntr=1, ig=-1,
ntpr=100, ntwr=10000,ntwx=100,
dt=0.002,nmropt=1,
ntb=2,ntp=2,taup=2.0,cut=10.0,
ioutfm=1,
/
&wt type='TEMP0', istep1=0, istep2=50000,
value1=100.0, value2=300.0 /
&wt type='END' /
Hold lipid fixed
10.0
RES 231 581
END
END
Then I did a production run by pmemd.cuda using the following parameters:
cuda.in
cal Production MD NVE with
GOOD energy conservation.
&cntrl
ntx=5, irest=1,
ntc=2, ntf=2, tol=0.000001,
nstlim=500000,
ntpr=2500, ntwx=2500,
ntwr=2500,
dt=0.002, cut=8.,
ntt=0, ntb=1, ntp=0,
ioutfm=1,
/
&ewald
dsum_tol=0.000001,
/
After 160 ps of MD run,It appears that the lipids in the system are falling
apart
I was wondering If anyone out there tells me what is going wrong here?
--
Gözde YALÇIN
Research Assistant
Rize Recep Tayyip Erdogan University
Faculty of Engineering
Bioengineering Department
53100 Rize-Turkey
Ph.D. Student in Biotechnology
Ankara University
Biotechnology Institute
06110 Besevler/Ankara-Turkey
05065055074
Prof Cenk(Jenk) ANDAC
Drug Discovery Lab. in Mevlana University
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Received on Wed Feb 12 2014 - 06:30:03 PST
