Here I am minimizating first Hydrogen only because of all the close contact are
due to added Hydrogen by leap.
> Hello,
>
> On Sat, Jun 19, 2010 at 3:59 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>> Ya I have seen the tutorial for simulation of DNA in implicit solvant
>
>
> There is no tutorial for "constant pH" simulations specifically, though it
> is not much different than other implicit solvent simulations
>
>
>> there is relaxing the DNA before MD simulation at tempi = 300.0, temp0 =
>> 300.0.
>> But actualy in one of the reply of my mail I got about heating and
>> equilibration
>> so thats why I have confusion.
>> For constant pH simulation I am donig the following step is it correct or
>> not?
>> 1)minimization:
>> a)minimization of hydrogen only (by mistake I my earlier mail I have wrote
>> that i hvae apply restraint on hydrogen).
>>
>
> I would not minimize just the hydrogens. The hydrogen distances won't
> change due to SHAKE, so I don't think you gain much by this step.
>
>
>> b)minimization of whole system
>>
>
> This seems to me to be the only minimization you really need. It doesn't
> need to be long, either, since it's just relaxing bad contacts. You may
> also add restraints to the backbone atoms to prevent any kind of major
> distortion of secondary structure.
>
>
>>
>> 2)heating (now which I will not do) and equilibration at tempi = 300.0,
>> temp0 =
>> 300.0
>>
>
> You certainly need to heat. And apply restraints to the backbone atoms like
> I've suggested, most likely. I have, on occasion, seen the entire protein
> unravel during heating, though that could be due to a couple bugs that were
> patched up in the constant pH code (make sure you apply all of these bug
> fixes! 47 for amber9 and 25 for amber10). In any case, I think it's a good
> idea to apply some restraints to the backbone while you're heating and
> equilibrating.
>
>
>>
>> 3)production run.
>>
>
> You can take off all restraints here and just run freely.
>
>
> Good luck!
> Jason
>
>
>>
>> >> Now I have to euqilibrat it with heating 0 - 300K.
>> >
>> > Have you looked at the tutorials?
>> >
>> > Bill
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 19 2010 - 14:00:03 PDT
