Hi Gozde,
We'll be adding Cholesterol parameters to Lipid14 shortly. In the meantime
one could use the lipid11 Cholesterol parameters but I don't know how well
they will perform with Lipid14. Shouldn't be too unreasonable.
With regards to the water - it just sounds like you aren't reimaging your
trajectory. AMBER (unless you set iwrap=1) just tracks the original
position of molecules even though they are reimaged mathematically. This
means it looks like water is slowly spreading out. You can use the
autoimage command in cpptraj to reimage things and create an imaged
trajectory which will show you what the unit cell looks like.
All the best
Ross
On 2/25/14, 9:43 AM, "Gözde YALÇIN" <yalcingozde88.gmail.com> wrote:
>Dear Prof. Walker and Callum Dickson
>As a follow up to your suggestions, a 20 ns of production run (with all
>restraints removed) was implemented using the lipid11 forces field for the
>membrane part.
>I attached a snapshot of the final step of the simulation.
>Overall the production run went well (I guess!!), but there still seems
>something weird.
>Although the membrane and the protein+ligand complex seem to hold
>together,
>this time the water layers above and below the membrane expanded
>horizontally way too much, leaving the box ..
>Is that expected for membrane simulations?
>Is there a way to post-process water molecules in the trajectory so that
>waters get back to the box.
> Lastly, I tried parameterizing the membrane system using the lipid14
>force field previously provided by Prof. Walker (Thanks again!). My
>membrane system includes some cholesterol molecules. It appear that the
>lipid14 force field does not include parameters for cholesterol. I was
>wondering if you could also provide me with a cholesterol OFF file.
>My best regards,
> Gözde Yalçžn
> Res. Asst. in Drug Development Laboratory of Prof. Jenk Andac
>
>
>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_201
>>4-
>> 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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>
>
>
>--
>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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Received on Tue Feb 25 2014 - 10:00:06 PST
