Dear Prof. Walker,
Thank you for making lipid14 force field available to us.
I now would like to run additional membrane simulations using AMBER FF14SB
and lipid14 force fields.
Based on your previous suggestions (see below),
I guess I do not need to use
*NPgammaT with a constant surface tension termfor NPT simulations of
membranes when lipid14 FF is used.*
*In that case, whould that be OK to use the following MD production run
parameters for NPT simulations of membranes :*&cntrl
imin=0, ntx=5, irest=1,
ntc=2, ntf=2, tol=0.0000001,
nstlim=2500000, ntt=3, gamma_ln=1.0,
temp0=300.0,
ntpr=5000, ntwr=5000, ntwx=5000,
dt=0.002, ig=-1,
ninterface=2,
ntb=2, ntp=2, cut=10.0, ioutfm=1,
/
or else what changes should be made for the MD parameters above.
My 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
From: Ross Walker <ross.rosswalker.co.uk
<ross.rosswalker.co.uk?Subject=Re%3A%20%5BAMBER%5D%20Falling%20apart%20of%20membrane>>
Date: Tue, 25 Feb 2014 09:48:58 -0800
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, "G�zde YAL�IN" <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, *
*> G�zde Yal�žn *
*> Res. Asst. in Drug Development Laboratory of Prof. Jenk Andac *
*> *
*> *
*>2014-02-12 19:42 GMT+02:00 Ross Walker <ross.rosswalker.co.uk
<
http://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
<
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, "G�zde YAL�IN" <yalcingozde88.gmail.com
<
http://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 <
http://cuda.in>. *
*>> > *
*>> >relax.in <
http://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 <
http://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 <
http://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 <
http://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... *
*>> > *
*>> > *
*>> >-- *
*>> >G�zde YAL�IN *
*>> >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://AMBER.ambermd.org> *
*>> >
http://lists.ambermd.org/mailman/listinfo/amber
<
http://lists.ambermd.org/mailman/listinfo/amber> *
*>> *
*>> *
*>> *
*> *
*> *
*> *
*>-- *
*>G�zde YAL�IN *
*>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 Mon Jun 30 2014 - 08:00:02 PDT
