To follow up on what Callum says (I.e. your density equilibration is
nowhere near long enough) - NPT simulations with lipid 11 need to be
NPgammaT with a constant surface tension term. See the example in the
tutorials section of the AMBER website.
You may want to switch to Lipid14 - just released
https://dl.dropboxusercontent.com/u/708185/lipid14_force_field_params_2014-
01-30.tar.gz which should not require a constant surface tension term for
NPT. You should also probably be running the production run with
anisotropic NPT scaling unless you have specific reasons for wanting NVT.
All the best
Ross
On 2/12/14, 5:24 AM, "Gözde YALÇIN" <yalcingozde88.gmail.com> wrote:
>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
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
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Received on Wed Feb 12 2014 - 10:00:04 PST
