Thank you very much for your relevancy. Also thanks for Lipid14. I
will follow that way for solving of problem. Thank you again.
Cheers
2014-02-12 19:42 GMT+02:00 Ross Walker <ross.rosswalker.co.uk>:
> 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
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 Thu Feb 13 2014 - 03:00:02 PST
