Hi Gözde,
You will need to equilibrate your system in NPT for much longer than your current protocol before moving into NVE.
I can't really tell from your residue numbering, but during temp1.in and temp2.in you want to keep restraints on both the protein and the membrane. Then move into longer NPT with weak restraints on the protein only (maybe 5ns), then finally further NPT with no restraints (probably at least 20ns).
How long each stage of equilibration needs to be is for you to judge - check that the box size has reached stable dimensions before moving into constant volume.
Also, what lipid and lipid parameters are you using and how big is your membrane around the protein?
All the best,
Callum
________________________________________
From: amber-bounces.ambermd.org [amber-bounces.ambermd.org] on behalf of Gözde YALÇIN [yalcingozde88.gmail.com]
Sent: 12 February 2014 13:24
To: amber.ambermd.org
Subject: [AMBER] Falling apart of membrane
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 - 06:30:03 PST
