step 3 seems ok- maybe a picture would help us understand what you see.
make sure the ptraj imagine is done correctly. is the step 3 final
density ok? the pressure coupling is pretty weak.
On Thu, May 6, 2010 at 8:56 AM, mish <smncbr.gmail.com> wrote:
> Hi,
> Fixed means restrained. but used very tight restrain (restraint_wt=200.0).
> I used proper ensembles mentioned in literature. But I am copying detail of
> input file so that u can point out other mistakes too..
>
> ------------ -------Step 1 ---------------------------
> minimization of solvent molecules
> &cntrl
> imin=1,maxcyc=3000,ncyc=500,
> cut=10.0,ntb=1,
> ntc=1,ntf=1,
> ntpr=50,
> ntr=1, restraintmask=':1-266',
> restraint_wt=200.0,
> /
>
> ------------------- step 2 --------------------------
> heating system with fixed protein
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=300000,dt=0.001,
> ntc=2,ntf=2,
> cut=10.0, ntb=1,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> tempi=10.0, temp0=300,
> ntr=1, restraintmask=':1-266',
> restraint_wt=200.0,
> nmropt=1
> /
> &wt TYPE='TEMP0', istep1=0, istep2=250000,
> value1=10.1, value2=300, /
> &wt TYPE='END' /
>
> ------------------- step 3 --------------------------equilibrating water in
> the system with fixed protein
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=700000,dt=0.001,
> ntc=2,ntf=2,
> cut=10.0, ntb=2, ntp=1, taup=5.0,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> temp0=300,
> ntr=1, restraintmask=':1-266',
> restraint_wt=200.0,
> /
>
>
> and i can see that weired behavior after step 3, which i supposed to be
> proper equilibrated octahedral box after 70 ps equilibration.
>
> ....mish
>
>
> On Thu, May 6, 2010 at 2:28 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> you don't say the most important thing- did you use NVT or NPT in each
>> step? and when you say "fixed", do you mean frozen or restrained?
>>
>> On Thu, May 6, 2010 at 8:00 AM, mish <smncbr.gmail.com> wrote:
>> > Hi all :
>> >
>> > I am trying to do some MM-PB/SA calculation in my system. For
>> equilibration
>> > of the salivated system (octahedral TIP3P) i used the fallowing scheme-
>> > 1- Minimization of solvent molecules with fixed protein
>> > 2- Heating system with fixed protein (300 ps)
>> > 3- Equilibrating water in the system with fixed protein (700 ps)
>> > 4- Minimization of protein with with fixed water
>> > 5- Heating system with fixed water (300ps)
>> > 6- Equilibration of whole system without any restrain (10 ns)
>> >
>> > I found that the density in the step 6 is less than 1 for first few few
>> ps
>> > and then it adjust is very soon. When i look in adjustment of water
>> molecule
>> > after each step, I found a weird thing after step 3. I did imaging with
>> > ptraj and found that few planes of octahedral water-box have small well
>> > shaped arrangenemt of water. I am really surprised that why this
>> happened.
>> > Is it may be due to only 12A layer of water box, that PBC is showing
>> effcet
>> > of adgacent protein ?
>> >
>> > Reigards
>> >
>> > ..mish
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 06 2010 - 06:30:03 PDT
