Hi everyone,
I did minimization and heating with these parameters and there is no
problem at that part. However after 10 ps of pmemd.cuda run, it seems that
the lipids are falling apart as seen in the attached file. I was wondering
if I need to change parameters in cuda.in.
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,
/
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
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,
/
Can you help me to solve this problem.Thanks for your relevancy...
Best regards...
--
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
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Received on Wed Feb 12 2014 - 05:30:04 PST
